+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== ====== --i : Input images (in a star-file or a stack) --o : Output rootname General options ===== --angpix : Pixel size (in Angstroms) --i --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --K (1) : Number of references to be refined --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry groupInitial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --skip_align (false) : Skip orientational assignment (only classify)? --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --norm (false) : Perform normalisation-error correction? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --skip_align (false) : Skip orientational assignment (only classify)? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --norm (false) : Perform normalisation-error correction? --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --scale (false) : Perform intensity-scale corrections on image groups? ====== --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinementComputation --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step ===== --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --memory_per_thread (2) : Available RAM (in Gb) for each thread --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== src/ml_optimiser_mpi.cpp line: --pad (2) : Oversampling factor for the Fourier transforms of the references 173 --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ====== General options ===== --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --i : Input images (in a star-file or a stack) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --o : Output rootname --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --angpix : Pixel size (in Angstroms) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) --iter (50) : Maximum number of iterations to perform --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --K (1) : Number of references to be refined --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --offset (3) : Initial estimated stddev for the origin offsets ===== --ctf (false) : Perform CTF correction? --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --norm (false) : Perform normalisation-error correction? : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : --memory_per_thread (2) : Available RAM (in Gb) for each thread --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --pad (2) : Oversampling factor for the Fourier transforms of the references --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? File: src/ml_optimiser_mpi.cpp line: 173 --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach ====== General options ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --i : Input images (in a star-file or a stack) Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --o : Output rootname Corrections ===== --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --angpix : Pixel size (in Angstroms) --ctf (false) : Perform CTF correction? --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --iter (50) : Maximum number of iterations to perform --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) --temp_ini (1000) : Initial temperature (K) for simulated annealing --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --temp_fin (1) : Initial temperature (K) for simulated annealing --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --norm (false) : Perform normalisation-error correction? MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --scale (false) : Perform intensity-scale corrections on image groups? 173 --flatten_solvent (false) : Perform masking on the references as well? ====== Computation ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) : Available RAM (in Gb) for each thread --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --verb (1) : Verbosity (1=normal, 0=silent) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration --random_seed (-1) : Number for the random seed generator ====== Orientations ===== --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --sym (c1) : Symmetry group --dont_check_norm (false) : Skip the check whether the images are normalised correctly --offset_range (6) : Search range for origin offsets (in pixels) --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --temp_fin (1) : Initial temperature (K) for simulated annealing --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 173 --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --skip_align (false) : Skip orientational assignment (only classify)? ====== General options ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --i : --ctf (false) : Perform CTF correction? Input images (in a star-file or a stack) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --o : Output rootname --angpix : Pixel size (in Angstroms) --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --iter (50) : Maximum number of iterations to perform --norm (false) : Perform normalisation-error correction? --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --scale (false) : Perform intensity-scale corrections on image groups? --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) ====== Computation ===== --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --j (1) : --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --pad (2) : Oversampling factor for the Fourier transforms of the references --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --verb (1) : Verbosity (1=normal, 0=silent) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --random_seed (-1) : Number for the random seed generator --sym (c1) : Symmetry group --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --offset_range (6) : Search range for origin offsets (in pixels) --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) --fix_sigma_offset (false) : Fix the stddev in the origin offsets? : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --temp_ini (1000) : Initial temperature (K) for simulated annealing --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --temp_fin (1) : Initial temperature (K) for simulated annealing Corrections ===== --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --ctf (false) : Perform CTF correction? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false)File: src/ml_optimiser_mpi.cpp line: : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : 173 Perform normalisation-error correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --i : Input images (in a star-file or a stack) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --o : Output rootname Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --angpix : Pixel size (in Angstroms) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --K (1) : Number of references to be refined --particle_diameter (-1) : ====== Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? General options ===== --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --i : Input images (in a star-file or a stack) --o : Output rootname --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --angpix : Pixel size (in Angstroms) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --iter (50) : Maximum number of iterations to perform --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1)Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --skip_align (false) : Skip orientational assignment (only classify)? --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc====== Corrections ===== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : --scale (false) : Perform intensity-scale corrections on image groups? ====== Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) Computation ===== --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : --j (1) : Number of threads to run in parallel (only useful on multi-core machines) Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --memory_per_thread (2) : Available RAM (in Gb) for each thread --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --pad (2) : Oversampling factor for the Fourier transforms of the references --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --verb (1) : Verbosity (1=normal, 0=silent) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) File: src/ml_optimiser_mpi.cpp line: --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 173 --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing General options ===== --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --i : Input images (in a star-file or a stack) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --o : Output rootname --angpix : Pixel size (in Angstroms) 173 --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? General options ===== --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --i : Input images (in a star-file or a stack) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --o : Output rootname --angpix : Pixel size (in Angstroms) --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --iter (50) : Maximum number of iterations to perform --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? ====== Corrections ===== --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --ctf (false) : Perform CTF correction? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? --ctf (false) : Perform CTF correction? ====== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? Computation ===== --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pad (2) : Oversampling factor for the Fourier transforms of the references --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --i : Input images (in a star-file or a stack) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : --o : Output rootname Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --angpix : Pixel size (in Angstroms) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --iter (50) : Maximum number of iterations to perform --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --offset (3) : Initial estimated stddev for the origin offsets --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread Limited tilt angle: positive for keeping side views, negative for keeping top views --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --sym (c1) : Symmetry group --offset_range (6) : --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10)Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : --auto_refine (false) : Perform 3D auto-refine procedure? Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform Computation ===== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --pad (2) : Oversampling factor for the Fourier transforms of the references --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --verb (1) : Verbosity (1=normal, 0=silent) --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --print_symmetry_ops (false) : --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation : Initial temperature (K) for simulated annealing --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing 173 --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) Output rootname --angpix : Pixel size (in Angstroms) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== InitialisationPerform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== ====== Initialisation ===== --ref (None) : --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) Skip orientational assignment (only classify)? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? : Perform CTF correction? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) Corrections ===== --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : --i : Input images (in a star-file or a stack) --o : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --ctf (false) : --pad (2) : Oversampling factor for the Fourier transforms of the references Output rootname --angpix : Pixel size (in Angstroms) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --iter (50) : Maximum number of iterations to perform --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views File: src/ml_optimiser_mpi.cpp line: --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) 173 --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure?-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --i : Input images (in a star-file or a stack) --o : --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Output rootname --angpix : Pixel size (in Angstroms) Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --iter (50) : Maximum number of iterations to perform --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) Corrections ===== --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --ctf (false) : --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? File: src/ml_optimiser_mpi.cpp line: 173 --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? 173 --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) Output rootname --angpix : Pixel size (in Angstroms) --iter (50)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : --o : Output rootname Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --angpix : Pixel size (in Angstroms) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --iter (50) : Maximum number of iterations to perform --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --K (1) : Number of references to be refined --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --split_random_halves (false) : Refine two random halves of the data completely separately --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --skip_align (false) : Skip orientational assignment (only classify)? --offset (3) : Initial estimated stddev for the origin offsets --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : --sym (c1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5)Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --perturb (0.5) : --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --i : Input images (in a star-file or a stack) --o : Output rootname --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --skip_align (false) : Skip orientational assignment (only classify)? --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately Corrections ===== --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --ctf (false) : --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== Perform CTF correction? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Corrections ===== --ctf (false) : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : --ctf (false) : Perform CTF correction? Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --norm (false) : Perform normalisation-error correction? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --i : Input images (in a star-file or a stack) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --o : Output rootname --angpix : Pixel size (in Angstroms) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) ====== Expert options ===== --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --verb (1) : Verbosity (1=normal, 0=silent) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --temp_ini (1000) : Initial temperature (K) for simulated annealing --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --temp_fin (1) : Initial temperature (K) for simulated annealing --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf (false) : Perform CTF correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --i : Input images (in a star-file or a stack) General options ===== --o : --i : Input images (in a star-file or a stack) Output rootname --angpix : Pixel size (in Angstroms) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --iter (50) : Maximum number of iterations to perform --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientationsPerform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) --sym (c1) : Symmetry group : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) Corrections ===== --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --ctf (false) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== : Skip orientational assignment (only classify)? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== ====== Corrections ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --pool (8) : Number of images to be processed together --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling ====== Expert options ===== --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --pad (2) : Oversampling factor for the Fourier transforms of the references --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --random_seed (-1) : Number for the random seed generator --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false)173 : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --i : Input images (in a star-file or a stack) --angpix : Pixel size (in Angstroms) --o : Output rootname --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --skip_rotate (false) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --ctf (false) : Perform CTF correction? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator ====== Computation ===== --j (1) : --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --pool (8) --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --pad (2) : Oversampling factor for the Fourier transforms of the references --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator 173 --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false)General options ===== : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --i : Input images (in a star-file or a stack) --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --o : Output rootname --angpix : Pixel size (in Angstroms) --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 173 --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) General options ===== --i : Input images (in a star-file or a stack) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --o : Output rootname --angpix : Pixel size (in Angstroms) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : --K (1) : Number of references to be refined --particle_diameter (-1)Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --offset_range (6) : Search range for origin offsets (in pixels) --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --skip_align (false) : Skip orientational assignment (only classify)? --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: ====== Corrections ===== 173 --ctf (false) : Perform CTF correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) General options ===== --norm (false) : Perform normalisation-error correction? --scale (false) --i : : Perform intensity-scale corrections on image groups? ====== Computation ===== Input images (in a star-file or a stack) --o : Output rootname --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --pool (8) : Number of images to be processed together --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --pad (2) : Oversampling factor for the Fourier transforms of the references --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --verb (1) : Verbosity (1=normal, 0=silent) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top viewsFraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --temp_ini (1000) : Initial temperature (K) for simulated annealing --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? File: src/ml_optimiser_mpi.cpp line: --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 173 --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== ====== General options ===== --i-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- : Input images (in a star-file or a stack) --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --iter (50) : Maximum number of iterations to perform --K (1) : Number of references to be refined --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --offset (3) : Initial estimated stddev for the origin offsets --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --offset_range (6) : Search range for origin offsets (in pixels) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --sym (c1) : Symmetry group --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --offset_range (6) : Search range for origin offsets (in pixels) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? ====== Corrections ===== --skip_rotate (false) : --ctf (false) : Perform CTF correction? Skip rotational assignment (only translate and classify)? ====== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Corrections ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ : Input images (in a star-file or a stack) --o : Output rootname ====== General options ===== --i : Input images (in a star-file or a stack) --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : --o : Output rootname --angpix : Pixel size (in Angstroms) Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --iter (50) : Maximum number of iterations to perform --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --sym (c1) : Symmetry group --offset_range (6) --offset (3) : Initial estimated stddev for the origin offsets : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --sym (c1) : Symmetry group --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --offset_range (6) : Search range for origin offsets (in pixels) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : --norm (false) : Perform normalisation-error correction? Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --skip_align (false) : Skip orientational assignment (only classify)? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : CorrectionsFraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? ===== --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --ctf (false) : Perform CTF correction? --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --temp_ini (1000) : Initial temperature (K) for simulated annealing --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --norm (false) : Perform normalisation-error correction? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Computation ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --o : Output rootname --angpix : Pixel size (in Angstroms) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --skip_align (false) : Skip orientational assignment (only classify)? --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? File: src/ml_optimiser_mpi.cpp line: --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? 173 --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --i : Input images (in a star-file or a stack) --o : Output rootname --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) ====== Computation ===== --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None)Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --pad (2) : Oversampling factor for the Fourier transforms of the references --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --verb (1) : Verbosity (1=normal, 0=silent) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) --random_seed (-1) : Number for the random seed generator : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) : Skip orientational assignment (only classify)? --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Fix the stddev in the origin offsets? Corrections ===== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --ctf (false) : Perform CTF correction? --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) --dont_check_norm (false) : Skip the check whether the images are normalised correctly : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : --temp_ini (1000) : Initial temperature (K) for simulated annealing Number of threads to run in parallel (only useful on multi-core machines) --temp_fin (1) : Initial temperature (K) for simulated annealing --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1)src/ml_optimiser_mpi.cpp line: : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 173 --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --i : General options ===== --i : Input images (in a star-file or a stack)Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : Output rootname --iter (50) : Maximum number of iterations to perform --angpix : Pixel size (in Angstroms) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --iter (50) : Maximum number of iterations to perform --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --K (1) : Number of references to be refined --particle_diameter (-1) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sym (c1) : Symmetry group --offset_range (6) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --sym (c1) : Symmetry group --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : --skip_align (false) : Skip orientational assignment (only classify)? Skip rotational assignment (only translate and classify)? ====== Corrections ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? ====== Corrections ===== --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing 173 --temp_fin (1) : Initial temperature (K) for simulated annealing +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) ====== --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files General options ===== MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --i : Input images (in a star-file or a stack)173 --o : Output rootname --angpix : Pixel size (in Angstroms) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --iter (50) : Maximum number of iterations to perform +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) General options ===== --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : --norm (false) : Perform normalisation-error correction? --scale (false) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views Perform intensity-scale corrections on image groups? ====== --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) Computation ===== --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --verb (1) : Verbosity (1=normal, 0=silent) Corrections ===== --ctf (false) : Perform CTF correction? --random_seed (-1) : Number for the random seed generator --coarse_size (-1) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --scale (false) : Perform intensity-scale corrections on image groups? ====== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit Computation ===== --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc --temp_ini (1000) : Initial temperature (K) for simulated annealing ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator File: src/ml_optimiser_mpi.cpp line: --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 173 --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false)-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) ++++++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : ====== Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== General options ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread General options ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- General options ===== General options ===== --i : Input images (in a star-file or a stack) --i : --o : Output rootname --angpix : Pixel size (in Angstroms) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) General options ===== --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --i : --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) Input images (in a star-file or a stack) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --o : Output rootname --angpix : Pixel size (in Angstroms) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --iter (50) : Maximum number of iterations to perform --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --skip_align (false) : Skip orientational assignment (only classify)? --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) Computation ===== --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --j (1) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== Input images (in a star-file or a stack) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --o : Output rootname --angpix : Pixel size (in Angstroms) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --K (1) : Number of references to be refined --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== OrientationsMlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2)173 : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --i : Input images (in a star-file or a stack) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --o : Output rootname --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --norm (false) : Perform normalisation-error correction? --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) ====== Corrections ===== --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) --norm (false) : Perform normalisation-error correction? : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --scale (false) : --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) Perform intensity-scale corrections on image groups? ====== Computation ===== --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --pad (2) : Oversampling factor for the Fourier transforms of the references --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --verb (1) : Verbosity (1=normal, 0=silent) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --temp_ini (1000) : Initial temperature (K) for simulated annealing --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing File: src/ml_optimiser_mpi.cpp line: --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 173 --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== 173 --j (1) : Number of threads to run in parallel (only useful on multi-core machines)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --memory_per_thread (2) : Available RAM (in Gb) for each thread General options ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --i : Input images (in a star-file or a stack) --pad (2) : Oversampling factor for the Fourier transforms of the references --o : Output rootname --angpix : Pixel size (in Angstroms) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : --verb (1) : Verbosity (1=normal, 0=silent) Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --offset (3) : Initial estimated stddev for the origin offsets --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 173 --sym (c1) : Symmetry group -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refinedOutput rootname --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --angpix : Pixel size (in Angstroms) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches Computation ===== --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --ctf (false) : Perform CTF correction? --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== ComputationFix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit ===== --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : --j (1)Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references 173 --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --ctf (false) : Perform CTF correction? General options ===== --ctf_intact_first_peak (false) --i : Input images (in a star-file or a stack) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --o : Output rootname --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --angpix : Pixel size (in Angstroms) Computation ===== --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) --temp_fin (1) : Initial temperature (K) for simulated annealing : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: ====== Corrections ===== --ctf (false) : Perform CTF correction? 173 --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --i : Input images (in a star-file or a stack) ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) Output rootname --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --angpix : Pixel size (in Angstroms) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : --skip_align (false) : Skip orientational assignment (only classify)? Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling ====== --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? Corrections ===== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) --ctf (false) : Perform CTF correction? : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) ====== General options ===== --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --i : Input images (in a star-file or a stack) --o : Output rootname --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly Computation ===== --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 173 --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== General options ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --memory_per_thread (2) : Available RAM (in Gb) for each thread +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --i : --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --o : Output rootname --angpix : Pixel size (in Angstroms) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --pool (8) : Number of images to be processed together --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : --i : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) Input images (in a star-file or a stack) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --o : --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) Output rootname --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --angpix : Pixel size (in Angstroms) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --iter (50) : Maximum number of iterations to perform --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Corrections ===== Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) --ctf (false) : : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) 173 --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++====== General options ===== ====== General options ===== --i : Input images (in a star-file or a stack) --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --o : --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) Output rootname --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --angpix : Pixel size (in Angstroms) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --iter (50) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) : Maximum number of iterations to perform --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --K (1) : Number of references to be refined --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --flatten_solvent (false) : Perform masking on the references as well? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) --offset_range (6) : Search range for origin offsets (in pixels) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ctf (false) : Perform CTF correction? --sym (c1) : Symmetry group --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --offset_range (6) : Search range for origin offsets (in pixels) --norm (false) : Perform normalisation-error correction? --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --j (1) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --pad (2) : Oversampling factor for the Fourier transforms of the references ====== --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10)Corrections ===== : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --ctf (false) : --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) Perform CTF correction? --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --norm (false) : Perform normalisation-error correction? --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files --j (1) : Number of threads to run in parallel (only useful on multi-core machines) MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --memory_per_thread (2) : Available RAM (in Gb) for each thread 173 --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- General options ===== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --i : --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== Input images (in a star-file or a stack) --ctf (false) : Perform CTF correction? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread General options ===== --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --i : Input images (in a star-file or a stack) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --ctf (false) : Perform CTF correction? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: General options ===== General options ===== --i : Input images (in a star-file or a stack) --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --sym (c1) : Symmetry group --offset_range (6) : --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) ====== Corrections ===== --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --ctf (false) : Perform CTF correction? --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : --j (1) : Number of threads to run in parallel (only useful on multi-core machines) Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --memory_per_thread (2) : Available RAM (in Gb) for each thread --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) --pad (2) : Oversampling factor for the Fourier transforms of the references : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --verb (1) : Verbosity (1=normal, 0=silent) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --random_seed (-1) : Number for the random seed generator --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 173 --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --i : --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== Input images (in a star-file or a stack) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) General options ===== --o : Output rootname --i --angpix : Pixel size (in Angstroms) --iter (50) : Input images (in a star-file or a stack) --o : Output rootname : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --angpix : Pixel size (in Angstroms) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) --iter (50) : Maximum number of iterations to perform : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --K (1) : Number of references to be refined --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --ctf (false) : Perform CTF correction? --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --sym (c1) : Symmetry group --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --offset_range (6) : Search range for origin offsets (in pixels) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false)Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) --norm (false) : Perform normalisation-error correction? : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () --scale (false) : Perform intensity-scale corrections on image groups? ====== : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: Computation ===== 173 --j (1) : Number of threads to run in parallel (only useful on multi-core machines) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++Corrections ===== ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --ctf (false) : Perform CTF correction? Corrections ===== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --ctf (false) : Perform CTF correction? --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname Output rootname --angpix : Pixel size (in Angstroms) --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --K (1) : Number of references to be refined --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant)====== Initialisation ===== --ref (None) : --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --offset_range (6) : Search range for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) Corrections ===== --ctf (false) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== : Perform CTF correction? Corrections ===== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ --norm (false) : Perform normalisation-error correction? ====== General options ===== --i : Input images (in a star-file or a stack) --o : --scale (false) : Perform intensity-scale corrections on image groups? ====== Output rootname --angpix : Pixel size (in Angstroms)Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --iter (50) : Maximum number of iterations to perform --memory_per_thread (2) : Available RAM (in Gb) for each thread --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --K (1) : Number of references to be refined --particle_diameter (-1) --pad (2) : Oversampling factor for the Fourier transforms of the references : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : --tau (None) : STAR file with input tau2-spectrum (to be kept constant) Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --offset (3) : Initial estimated stddev for the origin offsets --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --temp_ini (1000) : Initial temperature (K) for simulated annealing --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --temp_fin (1) : Initial temperature (K) for simulated annealing --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : --sym (c1) : Symmetry group Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) File: src/ml_optimiser_mpi.cpp line: --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 173 --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1)+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? ====== General options ===== --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --i : Input images (in a star-file or a stack) --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --o : Output rootname --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --angpix : Pixel size (in Angstroms) --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --norm (false) : Perform normalisation-error correction? --K (1) : Number of references to be refined --norm (false) --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) : Perform normalisation-error correction? --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : --scale (false)Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) : Perform intensity-scale corrections on image groups? ====== Computation ===== --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : --memory_per_thread (2) : Available RAM (in Gb) for each thread Refine two random halves of the data completely separately --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --pad (2) : Oversampling factor for the Fourier transforms of the references --offset (3) : Initial estimated stddev for the origin offsets --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) : Fraction of the weights to be considered in the first pass of adaptive oversampling --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --sym (c1) : Symmetry group --fix_sigma_noise (false) : Fix the experimental noise spectra? --offset_range (6) : Search range for origin offsets (in pixels) --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --temp_ini (1000) : Initial temperature (K) for simulated annealing --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : --temp_fin (1) : Initial temperature (K) for simulated annealing Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () --skip_align (false) : Skip orientational assignment (only classify)? : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== File: src/ml_optimiser_mpi.cpp line: 173 --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) Computation ===== --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --memory_per_thread (2) : Available RAM (in Gb) for each thread --verb (1) : Verbosity (1=normal, 0=silent) --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --random_seed (-1) : Number for the random seed generator --pad (2) : Oversampling factor for the Fourier transforms of the references --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --verb (1) : Verbosity (1=normal, 0=silent) --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) --temp_fin (1) : Initial temperature (K) for simulated annealing : Fix the experimental noise spectra? --fix_sigma_offset (false) : --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit File: src/ml_optimiser_mpi.cpp line: --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly 173 --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files General options ===== MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: --i : Input images (in a star-file or a stack) 173 --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== General options ===== --i : Input images (in a star-file or a stack) --o : Output rootname --angpix : Pixel size (in Angstroms) --iter (50) : Maximum number of iterations to perform --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) --K (1) : Number of references to be refined --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) --flatten_solvent (false) : Perform masking on the references as well? --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) --solvent_mask2 (None) : User-provided secondary mask (with its own average density) --tau (None) : STAR file with input tau2-spectrum (to be kept constant) --split_random_halves (false) : Refine two random halves of the data completely separately --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations ====== Initialisation ===== --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) --offset (3) : Initial estimated stddev for the origin offsets --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration ====== Orientations ===== --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views --sym (c1) : Symmetry group --offset_range (6) : Search range for origin offsets (in pixels) --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) --auto_refine (false) : Perform 3D auto-refine procedure? --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) --skip_align (false) : Skip orientational assignment (only classify)? --skip_rotate (false) : Skip rotational assignment (only translate and classify)? ====== Corrections ===== --ctf (false) : Perform CTF correction? --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) --norm (false) : Perform normalisation-error correction? --scale (false) : Perform intensity-scale corrections on image groups? ====== Computation ===== --j (1) : Number of threads to run in parallel (only useful on multi-core machines) --memory_per_thread (2) : Available RAM (in Gb) for each thread --pool (8) : Number of images to be processed together --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc ====== Expert options ===== --pad (2) : Oversampling factor for the Fourier transforms of the references --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation --verb (1) : Verbosity (1=normal, 0=silent) --random_seed (-1) : Number for the random seed generator --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) --fix_sigma_noise (false) : Fix the experimental noise spectra? --fix_sigma_offset (false) : Fix the stddev in the origin offsets? --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit --strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step --dont_check_norm (false) : Skip the check whether the images are normalised correctly --sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models? --temp_ini (1000) : Initial temperature (K) for simulated annealing --temp_fin (1) : Initial temperature (K) for simulated annealing --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) --scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program File: src/ml_optimiser_mpi.cpp line: 173 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --------------------------------------------------------------------------