diff --git a/generate_cli_docs.py b/generate_cli_docs.py new file mode 100644 index 0000000..96311a6 --- /dev/null +++ b/generate_cli_docs.py @@ -0,0 +1,92 @@ +import argparse +import pathlib +import subprocess +from textwrap import indent +import os +from typing import Iterable + + +def make_parser(): + """ + Returns the argument parser + """ + parser = argparse.ArgumentParser( + description="Produces a .rst documentation file describing the relion CLI, on stdout" + ) + parser.add_argument( + "relion_path", + help="Path to the relion binary. For example /path/to/bin/relion", + type=pathlib.Path, + ) + return parser + + +def skip_to_options(code: Iterable[str]) -> Iterable[str]: + """ + Skips all lines until the line containing +++ RELION, since the preceding lines + are largely useless + """ + found = False + for line in code: + if "+++ RELION" in line: + found = True + if found: + yield line + + +def filter_traceback(code: Iterable[str]) -> Iterable[str]: + """ + Remove the .cpp file traceback, since it contains the full user path + """ + for line in code: + if ".cpp, line" not in line: + yield line + + +def main(relion_path: pathlib.Path): + segments = [ + """ +Command Line Reference +====================== +""" + ] + binary_root = relion_path.parent + os.environ["PATH"] += ":" + str(binary_root) + for binary in binary_root.glob("relion_*"): + try: + result = subprocess.run( + [binary.name], capture_output=True, encoding="utf-8", shell=True + ) + # rst_output = docs_path / f'{binary}.rst' + header = f"``{binary.stem}``" + underline = "-" * (len(str(binary)) + 4) + # Remove the /path/to/bin from all help + raw_code = indent(result.stdout or result.stderr, prefix=" ").replace( + str(binary_root), "" + ) + code_lines = raw_code.splitlines() + # Remove the .cpp path + code_lines = list(filter_traceback(code_lines)) + if "+++ RELION" in raw_code: + # The first lines of some MPI commands have unnecessary info about the local machine's MPI setup + code_lines = skip_to_options(code_lines) + code = "\n".join(code_lines) + + segments.append( + f"""{header} +{underline} + +.. code-block:: text + +{code} +""" + ) + except FileNotFoundError: + pass + print("\n".join(segments)) + + +if __name__ == "__main__": + parser = make_parser() + args = parser.parse_args() + main(**vars(args)) diff --git a/source/Reference/Cli.rst b/source/Reference/Cli.rst new file mode 100644 index 0000000..105ae12 --- /dev/null +++ b/source/Reference/Cli.rst @@ -0,0 +1,2483 @@ + +Command Line Reference +====================== + +``relion_ctf_mask_test`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input particle *.star file + --s : Image size + --r : Particle radius + --t : Frequency step + --tw : Filter step width + --o : Output path + --j (1) : Number of threads + --mg (0) : Micrograph index + --version : Print RELION version and exit + +``relion_particle_select`` +--------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file containing the source particles + --i_ref : Input STAR file containing reference particles + --angles (false) : Copy particle viewing angles from reference + --offsets (false) : Copy particle offsets from reference + --o (selected.star) : Output path + --version : Print RELION version and exit + +``relion_demodulate`` +---------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file with a list of particles + --out : Output path + --j (6) : Number of OMP threads + --r31 (false) : Write output in Relion-3.1 format + --version : Print RELION version and exit + +``relion_estimate_gain`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i : Input movie STAR file + --o : Output file name + --j (1) : Number of threads + --max_frames (-1) : Target number of frames to average (rounded to movies; -1 means use all) + --random (false) : Randomise the order of input movies before taking subset + --dont_invert (false) : Don't take the inverse but simply writes the sum + --eer_upsampling (2) : EER upsampling (1 = 4K or 2 = 8K) + --version : Print RELION version and exit + +``relion_ctf_refine`` +---------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file containing the particles + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --o : Output directory, e.g. CtfRefine/job041/ + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --only_do_unfinished (false) : Skip those steps for which output files already exist. + --ctf_pad (false) : Use larger box to calculate CTF and then downscale to mimic boxing operation in real space + --diag (false) : Write out diagnostic data (slower) + ====== Defocus fit options ===== + --fit_defocus (false) : Perform refinement of per-particle defocus values? + --fit_mode (fpmfm) : String of 5 characters describing whether to fit the phase shift (1), + defocus (2), astigmatism (3), spherical aberration (4) and B-factors (5) + per particle ('p'), per micrograph ('m') or to keep them fixed ('f') + during the per-micrograph CTF refinement. + --max_defocus_iters (100) : Maximum number of iterations for CTF refinement. + --bf0 (false) : Perform brute-force per-particle defocus search (as in RELION 3.0) prior + to the per-micrograph CTF refinement. + --bf1 (false) : Perform brute-force defocus search after CTF refinement. + --bf_only (false) : Skip CTF refinement and only perform a brute-force defocus search. + --bf_range (2000.) : Defocus scan range (in A) for brute-force search. + --legacy_astig (false) : Estimate independent per-particle astigmatism (from RELION 3.0) + --kmin_defocus (30.0) : Inner freq. threshold for defocus estimation [Angst] + ====== B-factor options ===== + --fit_bfacs (false) : Estimate CTF B-factors + --bfac_per_mg (false) : Estimate B-factors per micrograph, instead of per particle + --bfac_min_B (-30) : Minimal allowed B-factor + --bfac_max_B (300) : Maximal allowed B-factor + --bfac_min_scale (0.2) : Minimal allowed scale-factor (essential for outlier rejection) + --kmin_bfac (30.0) : Inner freq. threshold for B-factor estimation [Angst] + ====== Beam-tilt options ===== + --fit_beamtilt (false) : Perform refinement of beamtilt + --kmin_tilt (20.0) : Inner freq. threshold for beamtilt estimation [Å] + --odd_aberr_max_n (0) : Maximum degree of Zernike polynomials used to fit odd (i.e. antisymmetrical) aberrations + --xr0_t (-1) : Exclusion ring start [Å] - use to exclude dominant frequency (e.g. for helices) + --xr1_t (-1) : Exclusion ring end [Å] + ====== Symmetric aberrations options ===== + --fit_aberr (false) : Estimate symmetric aberrations + --kmin_aberr (20.0) : Inner freq. threshold for symmetrical aberration estimation [Å] + --even_aberr_max_n (4) : Maximum degree of Zernike polynomials used to fit even (i.e. symmetrical) aberrations + --xr0_a (-1) : Exclusion ring start [Å] + --xr1_a (-1) : Exclusion ring end [Å] + ====== Anisotropic magnification options ===== + --fit_aniso (false) : Estimate anisotropic magnification + --kmin_mag (20.0) : Inner freq. threshold for anisotropic magnification estimation [Angst] + --keep_astig (false) : Do not translate astigmatism into new coordinates + --part_astig (false) : Allow astigmatism to vary among the particles of a micrograph + ====== Computational options ===== + --j (1) : Number of (OMP) threads + --min_MG (0) : First micrograph index + --max_MG (-1) : Last micrograph index (default is to process all) + --debug (false) : Write debugging data + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_merge_particles`` +--------------------------------------------------------------------- + +.. code-block:: text + + usage: relion_merge_particles ... + +``relion_run_ctffind`` +----------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + ====== CTF estimation ===== + --i : STAR file with all input micrographs, or a unix wildcard to all micrograph files, e.g. "mics/*.mrc" + --use_noDW (false) : Estimate CTFs from rlnMicrographNameNoDW instead of rlnMicrographName (only after MotionCor2) + --o (CtfEstimate/) : Directory, where all output files will be stored + --only_make_star (false) : Don't estimate any CTFs, only join all logfile results in a STAR file + --only_do_unfinished (false) : Only estimate CTFs for those micrographs for which there is not yet a logfile with Final values. + --do_at_most (-1) : Only process up to this number of (unprocessed) micrographs. + --ctfWin (-1) : Size (in pixels) of a centered, squared window to use for CTF-estimation + ====== Microscopy parameters ===== + --CS (-1) : Spherical Aberration (mm) + --HT (-1) : Voltage (kV) + --AmpCnst (-1) : Amplitude constrast + --angpix (-1) : Pixel size in the input micrographs (A) + ====== CTFFIND parameters ===== + --ctffind_exe () : Location of ctffind executable (or through RELION_CTFFIND_EXECUTABLE environment variable) + --Box (512) : Size of the boxes to calculate FFTs + --ResMin (100) : Minimum resolution (in A) to include in calculations + --ResMax (7) : Maximum resolution (in A) to include in calculations + --dFMin (10000) : Minimum defocus value (in A) to search + --dFMax (50000) : Maximum defocus value (in A) to search + --FStep (250) : defocus step size (in A) for search + --dAst (0) : amount of astigmatism (in A) + ====== CTFFIND4 parameters ===== + --is_ctffind4 (false) : The provided CTFFIND executable is CTFFIND4 (version 4.1+) + --use_given_ps (false) : Use pre-calculated power spectra? + --do_movie_thon_rings (false) : Calculate Thon rings from movie frames? + --avg_movie_frames (1) : Average over how many movie frames (try to get 4 e-/A2) + --movie_rootname (_movie.mrcs) : Rootname plus extension for movies + --do_phaseshift (false) : Estimate the phase shift in the images (e.g. from a phase-plate) + --phase_min (0.) : Minimum phase shift (in degrees) + --phase_max (180.) : Maximum phase shift (in degrees) + --phase_step (10.) : Step in phase shift (in degrees) + --j (1) : Number of threads (for CTFIND4 only) + --fast_search (false) : Disable "Slower, more exhaustive search" in CTFFIND4.1 (faster but less accurate) + ====== Gctf parameters ===== + --use_gctf (false) : Use Gctf instead of CTFFIND to estimate the CTF parameters + --gctf_exe () : Location of Gctf executable (or through RELION_GCTF_EXECUTABLE environment variable) + --ignore_ctffind_params (false) : Use Gctf default parameters instead of CTFFIND parameters + --EPA (false) : Use equi-phase averaging to calculate Thon rinds in Gctf + --do_validation (false) : Use validation inside Gctf to analyse quality of the fit? + --extra_gctf_options () : Additional options for Gctf + --gpu () : Device ids for each MPI-thread, e.g 0:1:2:3 + --version : Print RELION version and exit + +``relion_preprocess_mpi`` +-------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : The STAR file with all (selected) micrographs to extract particles from + --coord_suffix () : The suffix for the coordinate files, e.g. "_picked.star" or ".box" + --coord_dir (ASINPUT) : The directory where the coordinate files are (default is same as micrographs) + --part_dir (Particles/) : Output directory for particle stacks + --part_star () : Output STAR file with all particles metadata + --reextract_data_star () : A _data.star file from a refinement to re-extract, e.g. with different binning or re-centered (instead of --coord_suffix) + --keep_ctfs_micrographs (false) : By default, CTFs from fn_data will be kept. Use this flag to keep CTFs from input micrographs STAR file + --reset_offsets (false) : reset the origin offsets from the input _data.star file to zero? + --recenter (false) : Re-center particle according to rlnOriginX/Y in --reextract_data_star STAR file + --recenter_x (0.) : X-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_y (0.) : Y-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_z (0.) : Z-coordinate (in pixel inside the reference) to recenter re-extracted data on + --ref_angpix (-1) : Pixel size of the reference used for recentering. -1 uses the pixel size of particles. + ====== Particle extraction ===== + --extract (false) : Extract all particles from the micrographs + --extract_size (-1) : Size of the box to extract the particles in (in pixels) + --premultiply_ctf (false) : Premultiply the micrograph/frame with its CTF prior to particle extraction + --premultiply_extract_size (-1) : Size of the box to extract the particles in (in pixels) before CTF premultiplication + --ctf_intact_first_peak (false) : When premultiplying with the CTF, leave frequencies intact until the first peak + --phase_flip (false) : Flip CTF-phases in the micrograph/frame prior to particle extraction + --extract_bias_x (0) : Bias in X-direction of picked particles (this value in pixels will be added to the coords) + --extract_bias_y (0) : Bias in Y-direction of picked particles (this value in pixels will be added to the coords) + --only_do_unfinished (false) : Extract only particles if the STAR file for that micrograph does not yet exist. + ====== Particle operations ===== + --project3d (false) : Project sub-tomograms along Z to generate 2D particles + --scale (-1) : Re-scale the particles to this size (in pixels) + --window (-1) : Re-window the particles to this size (in pixels) + --norm (false) : Normalise the background to average zero and stddev one + --no_ramp (false) : Just subtract the background mean in the normalisation, instead of subtracting a fitted ramping background. + --bg_radius (-1) : Radius of the circular mask that will be used to define the background area (in pixels) + --white_dust (-1) : Sigma-values above which white dust will be removed (negative value means no dust removal) + --black_dust (-1) : Sigma-values above which black dust will be removed (negative value means no dust removal) + --invert_contrast (false) : Invert the contrast in the input images + --operate_on () : Use this option to operate on an input image stack + --operate_out (preprocessed.mrcs) : Output name when operating on an input image stack + ====== Helix extraction ===== + --helix (false) : Extract helical segments + --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical segments) + --helical_tubes (false) : Extract helical segments from tube coordinates + --helical_nr_asu (1) : Number of helical asymmetrical units + --helical_rise (0.) : Helical rise (in Angstroms) + --helical_bimodal_angular_priors (false) : Add bimodal angular priors for helical segments + --helical_cut_into_segments (false) : Cut helical tubes into segments + ====== MPI options ===== + --max_mpi_nodes (8) : Limit the number of effective MPI nodes to protect from too heavy disk I/O (thus ignoring larger values from mpirun) + --version : Print RELION version and exit + +``relion_run_ctffind_mpi`` +--------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + ====== CTF estimation ===== + --i : STAR file with all input micrographs, or a unix wildcard to all micrograph files, e.g. "mics/*.mrc" + --use_noDW (false) : Estimate CTFs from rlnMicrographNameNoDW instead of rlnMicrographName (only after MotionCor2) + --o (CtfEstimate/) : Directory, where all output files will be stored + --only_make_star (false) : Don't estimate any CTFs, only join all logfile results in a STAR file + --only_do_unfinished (false) : Only estimate CTFs for those micrographs for which there is not yet a logfile with Final values. + --do_at_most (-1) : Only process up to this number of (unprocessed) micrographs. + --ctfWin (-1) : Size (in pixels) of a centered, squared window to use for CTF-estimation + ====== Microscopy parameters ===== + --CS (-1) : Spherical Aberration (mm) + --HT (-1) : Voltage (kV) + --AmpCnst (-1) : Amplitude constrast + --angpix (-1) : Pixel size in the input micrographs (A) + ====== CTFFIND parameters ===== + --ctffind_exe () : Location of ctffind executable (or through RELION_CTFFIND_EXECUTABLE environment variable) + --Box (512) : Size of the boxes to calculate FFTs + --ResMin (100) : Minimum resolution (in A) to include in calculations + --ResMax (7) : Maximum resolution (in A) to include in calculations + --dFMin (10000) : Minimum defocus value (in A) to search + --dFMax (50000) : Maximum defocus value (in A) to search + --FStep (250) : defocus step size (in A) for search + --dAst (0) : amount of astigmatism (in A) + ====== CTFFIND4 parameters ===== + --is_ctffind4 (false) : The provided CTFFIND executable is CTFFIND4 (version 4.1+) + --use_given_ps (false) : Use pre-calculated power spectra? + --do_movie_thon_rings (false) : Calculate Thon rings from movie frames? + --avg_movie_frames (1) : Average over how many movie frames (try to get 4 e-/A2) + --movie_rootname (_movie.mrcs) : Rootname plus extension for movies + --do_phaseshift (false) : Estimate the phase shift in the images (e.g. from a phase-plate) + --phase_min (0.) : Minimum phase shift (in degrees) + --phase_max (180.) : Maximum phase shift (in degrees) + --phase_step (10.) : Step in phase shift (in degrees) + --j (1) : Number of threads (for CTFIND4 only) + --fast_search (false) : Disable "Slower, more exhaustive search" in CTFFIND4.1 (faster but less accurate) + ====== Gctf parameters ===== + --use_gctf (false) : Use Gctf instead of CTFFIND to estimate the CTF parameters + --gctf_exe () : Location of Gctf executable (or through RELION_GCTF_EXECUTABLE environment variable) + --ignore_ctffind_params (false) : Use Gctf default parameters instead of CTFFIND parameters + --EPA (false) : Use equi-phase averaging to calculate Thon rinds in Gctf + --do_validation (false) : Use validation inside Gctf to analyse quality of the fit? + --extra_gctf_options () : Additional options for Gctf + --gpu () : Device ids for each MPI-thread, e.g 0:1:2:3 + --version : Print RELION version and exit + +``relion_prepare_subtomo`` +--------------------------------------------------------------------- + +.. code-block:: text + + + ### RELION 2.0 sub-tomogram averaging - 23:59, FEB 19, 2014 ### + # The original python script was written by Tanmay Bharat to support sub-tomogram averaging in RELION. + # This 'relion_prepare_subtomo' executable was written by Shaoda He in Sjors Scheres' lab. + # Please ensure that you have provided the directory containing IMOD executables 'extracttilts' and 'newstack' + # Please provide either CTFFIND or Gctf executable. + # Please report bugs and comments to tbharat@mrc-lmb.cam.ac.uk or scheres@mrc-lmb.cam.ac.uk + # Please read the documentation on the RELION wiki, several questions are answered there. + # This version can set defocus values above a certain tilt to the defocus value of the zero degree tilt. + # This version will write out all the CTF reconstruction commands in the master file. + # This version supports RELION 2.0 only. For compatibility with older RELION, please use the original python script. + # This version depends on IMOD executables (extracttilts, newstack) and CTFFIND or Gctf. + + ### RELION 2.0 sub-tomogram averaging - Usage (also refer to RELION wiki) ### + # Before running the program: + # 1. Create a directory 'Tomogram/tomo???' for each reconstructed 3D tomogram. + # 2. In each of the individual tomogram directories you need: + # a. tomo.mrc : the actual reconstructed tomogram. + # b. tomo.mrcs : the aligned tilt series in MRC-stack format (Please rename if they are in .st format!) + # c. tomo.star : a STAR file with at least 3 columns: _rlnCoordinateX, Y and Z. (e.g. STAR file generated by 'relion_helix_toolbox --interpo') + # OR (if STAR file exists then .coords file will be ignored) + # tomo.coords : a text file with 3 columns: the X, Y and Z coordinates of each subtomogram (e.g. save this from IMOD). + # d. tomo.order : a text file with 2 columns: the tilt angle of each image in tomo.mrcs and the accumulated dose in e-/A2 for that image. + # e. tomo.tlt : (OPTIONAL) a text file with the final tilt angles from IMOD. If this is not provided then the extended header of the .mrcs will be read. + # 3. Run the program. (Input files will be checked in the initialisation step. Please pay attention if error messages pop up.) + # 4. Check the contents of 'do_all_reconstruct_ctfs.sh', (split it into multiple files for parallelisation) and run the .sh script (please provide the reconstruction box size). + # 5. Process the data with RELION 2.0 GUI. + + ################################################################### + Checking input data ... + Calculated pixel size (10000 * DPix / Mag) = 2.18302 Angstrom(s) + === Backtrace === + relion_prepare_subtomo(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x7d) [0x55d9e2b8bb8d] + relion_prepare_subtomo(_ZN15prepare_subtomo13initialChecksEv+0x56cb) [0x55d9e2b8443b] + relion_prepare_subtomo(main+0xa7) [0x55d9e2b64257] + /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f353c0ead90] + /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f353c0eae40] + relion_prepare_subtomo(_start+0x25) [0x55d9e2b64765] + ================== + ERROR: + Cannot find IMOD 'extractilts' executable /public/EM/imod/imod-4.5.8/IMOD/bin/extracttilts + +``relion_mrc2vtk`` +------------------------------------------------------------- + +.. code-block:: text + + usage: relion_mrc2vtk X.(mrc/mrcs/tiff/spi) + -> X.vtk + +``relion_flex_analyse_mpi`` +---------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --data () : The _data.star file with the orientations to be analysed + --model () : The corresponding _model.star file with the refined model + --bodies () : The corresponding star file with the definition of the bodies + --o (analyse) : Output rootname + ====== 3D model options ===== + --3dmodels (false) : Generate a 3D model for each experimental particles + --size_3dmodels (-1) : Output size of the 3D models (default is same as input particles) + ====== PCA options ===== + --PCA_orient (false) : Perform a principal components analysis on the multibody orientations + --do_maps (false) : Generate maps along the principal components + --k (-1) : Number of principal components to generate maps for + --v (0.75) : Or use as many principal components to explain this fraction of variance (<0,1]) + --maps_per_movie (10) : Number of maps to use for the movie of each principal component + --bins (100) : Number of bins in histograms of the eigenvalues for each principal component + --select_eigenvalue (-1) : Output a selection particle.star file based on eigenvalues along this eigenvector + --select_eigenvalue_min (-99999.) : Minimum for eigenvalue to include particles in selection output star file + --select_eigenvalue_max (99999.) : Maximum for eigenvalue to include particles in selection output star file + --write_pca_projections (false) : Write out a text file with all PCA projections for all particles + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_postprocess_mpi`` +--------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input name of half1, e.g. run_half1_class001_unfil.mrc + --i2 () : Input name of half2, (default replaces half1 from --i with half2) + --o (postprocess) : Output rootname + --angpix (-1) : Pixel size in Angstroms + --half_maps (false) : Write post-processed half maps for validation + --mtf_angpix (-1.) : Pixel size in the original micrographs/movies (in Angstroms) + --molweight (-1) : Molecular weight (in kDa) of ordered protein mass + ====== Masking options ===== + --auto_mask (false) : Perform automated masking, based on a density threshold + --inimask_threshold (0.02) : Density at which to threshold the map for the initial seed mask + --extend_inimask (3.) : Number of pixels to extend the initial seed mask + --width_mask_edge (6.) : Width for the raised cosine soft mask edge (in pixels) + --mask () : Filename of a user-provided mask (1=protein, 0=solvent, all values in range [0,1]) + --force_mask (false) : Use the mask even when the masked resolution is worse than the unmasked resolution + ====== Sharpening options ===== + --mtf () : User-provided STAR-file with the MTF-curve of the detector + --auto_bfac (false) : Perform automated B-factor determination (Rosenthal and Henderson, 2003) + --autob_lowres (10.) : Lowest resolution (in A) to include in fitting of the B-factor + --autob_highres (0.) : Highest resolution (in A) to include in fitting of the B-factor + --adhoc_bfac (0.) : User-provided B-factor (in A^2) for map sharpening, e.g. -400 + ====== Filtering options ===== + --skip_fsc_weighting (false) : Do not use FSC-weighting (Rosenthal and Henderson, 2003) in the sharpening process + --low_pass (0) : Resolution (in Angstroms) at which to low-pass filter the final map (0: disable, negative: resolution at FSC=0.143) + ====== Local-resolution options ===== + --locres (false) : Perform local resolution estimation + --locres_sampling (25.) : Sampling rate (in Angstroms) with which to sample the local-resolution map + --locres_maskrad (-1) : Radius (in A) of spherical mask for local-resolution map (default = 0.5*sampling) + --locres_edgwidth (-1) : Width of soft edge (in A) on masks for local-resolution map (default = sampling) + --locres_randomize_at (25.) : Randomize phases from this resolution (in A) + --locres_minres (50.) : Lowest local resolution allowed (in A) + ====== Expert options ===== + --ampl_corr (false) : Perform amplitude correlation and DPR, also re-normalize amplitudes for non-uniform angular distributions + --randomize_at_fsc (0.8) : Randomize phases from the resolution where FSC drops below this value + --randomize_at_A (-1) : Randomize phases from this resolution (in A) onwards (if positive) + --filter_edge_width (2) : Width of the raised cosine on the low-pass filter edge (in resolution shells) + --verb (1) : Verbosity + --random_seed (0) : Seed for random number generator (negative value for truly random) + --version : Print RELION version and exit + +``relion_refine`` +------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Input images (in a star-file) + --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) + --K (1) : Number of references to be refined + --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) + --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) + --flatten_solvent (false) : Perform masking on the references as well? + --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) + --solvent_mask2 (None) : User-provided secondary mask (with its own average density) + --lowpass_mask (None) : User-provided mask for low-pass filtering + --lowpass (0) : User-provided cutoff for region specified above + --tau (None) : STAR file with input tau2-spectrum (to be kept constant) + --local_symmetry (None) : Local symmetry description file containing list of masks and their operators + --split_random_halves (false) : Refine two random halves of the data completely separately + --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations + ====== Initialisation ===== + --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) + --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles + --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) + --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) + --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration + ====== Orientations ===== + --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) + --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc + --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) + --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views + --sym (c1) : Symmetry group + --relax_sym () : Symmetry to be relaxed + --offset_range (6) : Search range for origin offsets (in pixels) + --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) + --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (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) + --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) + --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) + --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) + --skip_align (false) : Skip orientational assignment (only classify)? + --skip_rotate (false) : Skip rotational assignment (only translate and classify)? + --bimodal_psi (false) : Do bimodal searches of psi angle? + ====== Helical reconstruction (in development...) ===== + --helix (false) : Perform 3D classification or refinement for helices? + --ignore_helical_symmetry (false) : Ignore helical symmetry? + --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) + --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) + --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) + --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) + --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) + --helical_rise_initial (0.) : Helical rise (in Angstroms) + --helical_rise_min (0.) : Minimum helical rise (in Angstroms) + --helical_rise_max (0.) : Maximum helical rise (in Angstroms) + --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) + --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) + --helical_z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix. Important in imposing and refining symmetry + --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) + --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) + --helical_symmetry_search (false) : Perform local refinement of helical symmetry? + --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks + --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? + --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) + --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector + ====== Corrections ===== + --ctf (false) : Perform CTF correction? + --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? + --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? + --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? + --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? + --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) + --norm (false) : Perform normalisation-error correction? + --scale (false) : Perform intensity-scale corrections on image groups? + --no_norm (false) : Switch off normalisation-error correction? + --no_scale (false) : Switch off intensity-scale corrections on image groups? + ====== Stochastic Gradient Descent ===== + --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization + --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users + --sgd_ini_iter (50) : Number of initial SGD iterations + --sgd_fin_iter (50) : Number of final SGD iterations + --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones + --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) + --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) + --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations + --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations + --mu (0.9) : Momentum parameter for SGD updates + --sgd_stepsize (0.5) : Step size parameter for SGD updates + --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) + --sgd_sigma2fudge_halflife (-1) : Initialise SGD with 8x higher noise-variance, and reduce with this half-life in # of particles (default is keep normal variance) + --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off + --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) + ====== Computation ===== + --pool (1) : Number of images to pool for each thread task + --j (1) : Number of threads to run in parallel (only useful on multi-core machines) + --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc + --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory + --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) + --preread_images (false) : Use this to let the leader process read all particles into memory. Be careful you have enough RAM for large data sets! + --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. + --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) + --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. + --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. + --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations + --gpu (false) : Use available gpu resources for some calculations + --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. + ====== Expert options ===== + --pad (2) : Oversampling factor for the Fourier transforms of the references + --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) + --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? + --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation + --verb (1) : Verbosity (1=normal, 0=silent) + --random_seed (-1) : Number for the random seed generator + --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach + --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling + --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) + --fix_sigma_noise (false) : Fix the experimental noise spectra? + --fix_sigma_offset (false) : Fix the stddev in the origin offsets? + --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement + --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit + --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit + --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step + --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step + --dont_check_norm (false) : Skip the check whether the images are normalised correctly + --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) + --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? + --skip_maximize (false) : Skip maximization step (only write out data.star file)? + --failsafe_threshold (40) : Maximum number of particles permitted to be handled by fail-safe mode, due to zero sum of weights, before exiting with an error (GPU only). + --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) + --auto_iter_max (999) : In auto-refinement, stop at this iteration. + --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. + --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. + --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. + --trust_ref_size (false) : Trust the pixel and box size of the input reference; by default the program will die if these are different from the first optics group of the data + --maxsig (-1) : Maximum number of poses & translations to consider + --skip_gridding (false) : Skip gridding in the M step + --version : Print RELION version and exit + +``relion_convert_to_tiff_mpi`` +------------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General Options ===== + --i : Input movie to be compressed (an MRC/MRCS file or a list of movies as .star or .lst) + --o (./) : Directory for output TIFF files + --only_do_unfinished (false) : Only process non-converted movies. + --j (1) : Number of threads (useful only for --estimate_gain) + --gain () : Estimated gain map and its reliablity map (read) + --thresh (50) : Number of success needed to consider a pixel reliable + --estimate_gain (false) : Estimate gain + ====== EER rendering options ===== + --eer_grouping (40) : EER grouping + --eer_upsampling (1) : EER upsampling (1 = 4K or 2 = 8K) + --short (false) : use unsigned short instead of signed byte for EER rendering + ====== TIFF writing options ===== + --compression (auto) : compression type (none, auto, deflate (= zip), lzw) + --deflate_level (6) : deflate level. 1 (fast) to 9 (slowest but best compression) + --ignore_error (false) : Don't die on un-expected defect pixels (can be dangerous) + --line_by_line (false) : Use one strip per row + --version : Print RELION version and exit + +``relion_reposition`` +---------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file containing the particles + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --max_shift (10) : Maximal allowed shift + --cc_pad (1) : Cross-correlation padding + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --j (1) : Number of (OMP) threads + --o (repositioned/) : Output path + --version : Print RELION version and exit + +``relion_reconstruct`` +----------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Input STAR file with the projection images and their orientations + --o (relion.mrc) : Name for output reconstruction + --sym (c1) : Symmetry group + --maxres (-1) : Maximum resolution (in Angstrom) to consider in Fourier space (default Nyquist) + --pad (2) : Padding factor + --img () : Optional: image path prefix + --subset (-1) : Subset of images to consider (1: only reconstruct half1; 2: only half2; other: reconstruct all) + --class (-1) : Consider only this class (-1: use all classes) + --angpix (-1) : Pixel size in the reconstruction (take from first optics group by default) + ====== CTF options ===== + --ctf (false) : Apply CTF correction + --ctf_intact_first_peak (false) : Leave CTFs intact until first peak + --ctf_phase_flipped (false) : Images have been phase flipped + --only_flip_phases (false) : Do not correct CTF-amplitudes, only flip phases + ====== Ewald-sphere correction options ===== + --ewald (false) : Correct for Ewald-sphere curvature (developmental) + --mask_diameter (-1.) : Diameter (in A) of mask for Ewald-sphere curvature correction + --width_mask_edge (3) : Width (in pixels) of the soft edge on the mask + --reverse_curvature (false) : Try curvature the other way around + --newbox (-1) : Box size of reconstruction after Ewald sphere correction + --sectors (2) : Number of sectors for Ewald sphere correction + --skip_mask (false) : Do not apply real space mask during Ewald sphere correction + --skip_weighting (false) : Do not apply weighting during Ewald sphere correction + ====== Helical options ===== + --nr_helical_asu (1) : Number of helical asymmetrical units + --helical_rise (0.) : Helical rise (in Angstroms) + --helical_twist (0.) : Helical twist (in degrees, + for right-handedness) + ====== Expert options ===== + --subtract () : Subtract projections of this map from the images used for reconstruction + --NN (false) : Use nearest-neighbour instead of linear interpolation before gridding correction + --blob_r (1.9) : Radius of blob for gridding interpolation + --blob_m (0) : Order of blob for gridding interpolation + --blob_a (15) : Alpha-value of blob for gridding interpolation + --iter (10) : Number of gridding-correction iterations + --refdim (3) : Dimension of the reconstruction (2D or 3D) + --angular_error (0.) : Apply random deviations with this standard deviation (in degrees) to each of the 3 Euler angles + --shift_error (0.) : Apply random deviations with this standard deviation (in Angstrom) to each of the 2 translations + --fom_weighting (false) : Weight particles according to their figure-of-merit (_rlnParticleFigureOfMerit) + --fsc () : FSC-curve for regularized reconstruction + --3d_rot (false) : Perform 3D rotations instead of backprojections from 2D images + --reconstruct_ctf (-1) : Perform a 3D reconstruction from 2D CTF-images, with the given size in pixels + --ctf2 (false) : Reconstruct CTF^2 and then take the sqrt of that + --skip_gridding (false) : Skip gridding part of the reconstruction + --debug () : Rootname for debug reconstruction files + --debug_ori_size (1) : Rootname for debug reconstruction files + --debug_size (1) : Rootname for debug reconstruction files + --reconstruct_noise () : Reconstruct noise using sigma2 values in this model STAR file + --read_weights (false) : Developmental: read freq. weight files + --write_debug_output (false) : Write out arrays with data and weight terms prior to reconstruct + --external_reconstruct (false) : Write out BP denominator and numerator for external_reconstruct program + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_find_tiltpairs`` +-------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General Options ===== + --u : STAR file with the untilted xy-coordinates + --t : STAR file with the untilted xy-coordinates + --size : Largest dimension of the micrograph (in pixels), e.g. 4096 + --acc : Allowed accuracy (in pixels), e.g. half the particle diameter + --dim (200) : Dimension of boxed particles (for EMAN .box files in pixels) + --tilt (99999.) : Fix tilt angle (in degrees) + --rot (99999.) : Fix direction of the tilt axis (in degrees), 0 = along y, 90 = along x + --dont_opt (false) : Skip optimization of the transformation matrix + ====== Specified tilt axis and translational search ranges ===== + --tilt0 (0.) : Minimum tilt angle (in degrees) + --tiltF (99999.) : Maximum tilt angle (in degrees) + --tiltStep (1.) : Tilt angle step size (in degrees) + --rot0 (0.) : Minimum rot angle (in degrees) + --rotF (99999.) : Maximum rot angle (in degrees) + --rotStep (1.) : Rot angle step size (in degrees) + --x0 (-99999) : Minimum X offset (pixels) + --xF (99999) : Maximum X offset (pixels) + --xStep (-1) : X offset step size (pixels) + --y0 (-99999) : Minimum Y offset (pixels) + --yF (99999) : Maximum Y offset (pixels) + --yStep (-1) : Y offset step size (pixels) + --version : Print RELION version and exit + +``relion_convert_star`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i (None) : Input STAR file to be converted + --o (None) : Output STAR file to be written + --Cs (-1) : Spherical aberration (mm) + --Q0 (-1) : Amplitude contrast + --version : Print RELION version and exit + ERROR: + Please specify input and output file names + === Backtrace === + relion_convert_star(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x7d) [0x55ef81a8f54d] + relion_convert_star(_ZN14star_converter4readEiPPc+0xb62) [0x55ef81a876b2] + relion_convert_star(main+0x86) [0x55ef81a86136] + /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f7d19878d90] + /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f7d19878e40] + relion_convert_star(_start+0x25) [0x55ef81a86955] + ================== + ERROR: + Please specify input and output file names + +``relion_run_motioncorr`` +-------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : STAR file with all input micrographs, or a Linux wildcard with all micrographs to operate on + --o (MotionCorr) : Name for the output directory + --j (1) : Number of threads per movie (= process) + --max_io_threads (-1) : Limit the number of IO threads. + --only_do_unfinished (false) : Only run motion correction for those micrographs for which there is not yet an output micrograph. + --do_at_most (-1) : Only process at most this number of (unprocessed) micrographs. + --grouping_for_ps (-1) : Group this number of frames and write summed power spectrum. -1 == do not write + --ps_size (512) : Output size of power spectrum + --first_frame_sum (1) : First movie frame used in output sum (start at 1) + --last_frame_sum (-1) : Last movie frame used in output sum (0 or negative: use all) + --eer_grouping (40) : EER grouping + --eer_upsampling (1) : EER upsampling (1 = 4K or 2 = 8K) + ====== MOTIONCOR2 options ===== + --use_motioncor2 (false) : Use Shawn Zheng's MOTIONCOR2. + --motioncor2_exe () : Location of MOTIONCOR2 executable (or through RELION_MOTIONCOR2_EXECUTABLE environment variable) + --bin_factor (1) : Binning factor (can be non-integer) + --bfactor (150) : B-factor (in pix^2) that will be used inside MOTIONCOR2 + --gainref () : Location of MRC file with the gain reference to be applied + --gain_rot (0) : Rotate the gain reference this number times 90 degrees clock-wise (in relion_display). This is same as MotionCor2's RotGain. 0, 1, 2 or 3 + --gain_flip (0) : Flip the gain reference. This is same as MotionCor2's FlipGain. 0, 1 (flip Y == upside down) or 2 (flip X == left to right) + --patch_x (1) : Patching in X-direction for MOTIONCOR2 + --patch_y (1) : Patching in Y-direction for MOTIONCOR2 + --group_frames (1) : Average together this many frames before calculating the beam-induced shifts + --defect_file () : Location of a MOTIONCOR2-style detector defect file (x y w h) or a defect map (1 means bad) + --archive () : Location of the directory for archiving movies in 4-byte MRC format + --other_motioncor2_args () : Additional arguments to MOTIONCOR2 + --gpu () : Device ids for each MPI-thread, e.g 0:1:2:3 + ====== Dose-weighting options ===== + --dose_weighting (false) : Use dose-weighting scheme + --angpix (-1) : Pixel size in Angstroms + --voltage (-1) : Voltage (in kV) for dose-weighting + --dose_per_frame (1) : Electron dose (in electrons/A2/frame) for dose-weighting + --preexposure (0) : Pre-exposure (in electrons/A2) for dose-weighting + ====== Own motion correction options ===== + --use_own (false) : Use our own implementation of motion correction + --skip_defect (false) : Skip hot pixel detection + --save_noDW (false) : Save aligned but non dose weighted micrograph + --max_iter (5) : Maximum number of iterations for alignment. Only valid with --use_own + --interpolate_shifts (false) : (EXPERIMENTAL) Interpolate shifts + --ccf_downsample (0) : (EXPERT) Downsampling rate of CC map. default = 0 = automatic based on B factor + --early_binning (false) : Do binning before alignment to reduce memory usage. This might dampen signal near Nyquist. (ON by default) + --no_early_binning (false) : Disable --early_binning + --dose_motionstats_cutoff (4.) : Electron dose (in electrons/A2) at which to distinguish early/late global accumulated motion in output statistics + --version : Print RELION version and exit + +``relion_star_loopheader`` +--------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_loopheader ... + + === Purpose: === + This (bash) script generates the header of STAR-file with the given labels + + === Example: === + /relion_star_loopheader rlnImageName rlnDefocusU rlnDefocusV rlnDefocusAngle rlnVoltage rlnSphericalAberration rlnAmplitudeContrast + yields: + data_ + loop_ + _rlnImageName + _rlnDefocusU + _rlnDefocusV + _rlnDefocusAngle + _rlnVoltage + _rlnSphericalAberration + _rlnAmplitudeContrast + +``relion_star_printtable`` +--------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_printtable [ ...] + + === Purpose: === + This (bash) script prints the contents of a datablock (with name tablename) from a starfile + If any labels are given, then only those will be printed + + === Example: === + /relion_star_printtable run3_it024_model.star data_model_class_1 rlnResolution rlnSsnrMap + (NOTE: not _rlnResolution) + + === Limitations: === + This program makes a temporary directory under $TMPDIR. This folder must be writable and have sufficient space. + + This program does not perform any error checks. + When specified table and/or column(s) are absent in the input, the program might give incorrect results. + In older versions, table names and column names could match only partially. For example, rlnFourierShellCorrelationCorrected matched rlnFourierShellCorrelation. This was dangerous and the match is exact now. + + To address these issues, this program will be completely re-written in the next major update (RELION 3.2). + In the new version, the errors are handled more strictly. Please update your scripts to prepare for transition. + + +``relion_mask_create`` +----------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Mask creation options ===== + --i () : Input map to use for thresholding to generate initial binary mask + --o (mask.mrc) : Output mask + --and () : Pixels in the initial mask will be one if the input AND this map are above the --ini_threshold value + --or () : Pixels in the initial mask will be one if the input OR this map are above the --ini_threshold value + --and_not () : Pixels in the initial mask will be one if the input is above the --ini_threshold AND this map is below it + --or_not () : Pixels in the initial mask will be one if the input is above the --ini_threshold OR this map is below it + --ini_threshold (0.01) : Initial threshold for binarization + --extend_inimask (0) : Extend initial binary mask this number of pixels + --width_soft_edge (0) : Width (in pixels) of the additional soft edge on the binary mask + --invert (false) : Invert the final mask + --helix (false) : Generate a mask for 3D helix + --lowpass (-1) : Lowpass filter (in Angstroms) for the input map, prior to binarization (default is none) + --angpix (-1) : Pixel size (in Angstroms) for the lowpass filter + --z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix + --j (1) : Number of threads + ====== De novo mask creation ===== + --denovo (false) : Create a mask de novo + --box_size (-1) : The box size of the mask in pixels + --inner_radius (0) : Inner radius of the masked region in pixels + --outer_radius (99999) : Outer radius of the mask region in pixels + --center_x (0) : X coordinate of the center of the mask in pixels + --center_y (0) : Y coordinate of the center of the mask in pixels + --center_z (0) : Z coordinate of the center of the mask in pixels + --version : Print RELION version and exit + +``relion_helix_inimodel2d`` +---------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --o () : Output rootname + --i () : STAR file with the input images and orientation parameters + ====== Parameters ===== + --crossover_distance () : Distance in Angstroms between 2 cross-overs + --iter (10) : Maximum number of iterations to perform + --K (1) : Number of classes + --angpix (-1) : Pixel size in Angstroms (default take from STAR file) + --maxres (-1) : Limit calculations to approximately this resolution in Angstroms + --search_shift (0) : How many Angstroms to search translations perpendicular to helical axis? + --search_angle (0) : How many degrees to search in-plane rotations? + --step_angle (1) : The step size (in degrees) of the rotational searches + --iniref () : An initial model to starting optimisation path + --sym (1) : Order of symmetry in the 2D xy-slice? + --smear (0) : Smear out each image along X to ensure continuity + --random_seed (-1) : Random seed (default is with clock) + --search_size (5) : Search this many pixels up/down of the target downscaled size to fit best crossover distance + --mask_diameter (-1) : The diameter (A) of a mask to be aplpied to the 2D reconstruction + --j (1) : Number of (openMP) threads + --only_make_3d (false) : Take the iniref image, and create a 3D model from that without any alignment of the input images + --version : Print RELION version and exit + +``relion_localsym_mpi`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Show usage ===== + --function_help (false) : Show usage for the selected function (JUN 30, 2017) + ====== Options ===== + --apply (false) : Apply local symmetry to a 3D cryo-EM density map + --duplicate (false) : Duplicate subunits/masks according to local symmetry operators + --search (false) : Local searches of local symmetry operators + --transform (false) : Transform a map according to three Euler angles and XYZ translations + --txt2rln (false) : Convert operators from DM to RELION STAR format + --debug (false) : (DEBUG ONLY) + ====== Parameters (alphabetically ordered) ===== + --angpix (1.) : Pixel size (in Angstroms) of input image + --ang_range (0.) : Angular search range of operators (in degrees), overwrite rot-tilt-psi ranges if set to positive + --ang_rot_range (0.) : Angular (rot) search range of operators (in degrees) + --ang_tilt_range (0.) : Angular (tilt) search range of operators (in degrees) + --ang_psi_range (0.) : Angular (psi) search range of operators (in degrees) + --ang_step (1.) : Angular search step of operators (in degrees) + --bin (-1.) : Binning factor (<= 1 means no binning) + --ini_threshold (0.01) : Initial threshold for binarization + --i_map () : Input 3D unsymmetrised map + --i_mask_info (maskinfo.txt) : Input file with mask filenames and rotational / translational operators (for local searches) + --i_op_mask_info (None) : Input file with mask filenames for all operators (for global searches) + --n (2) : Create this number of masks according to the input density map + --offset_range (0.) : Translational search range of operators (in Angstroms), overwrite x-y-z ranges if set to positive + --offset_x_range (0.) : Translational (x) search range of operators (in Angstroms) + --offset_y_range (0.) : Translational (y) search range of operators (in Angstroms) + --offset_z_range (0.) : Translational (z) search range of operators (in Angstroms) + --offset_step (1.) : Translational search step of operators (in Angstroms) + --o_map () : Output 3D symmetrised map + --o_mask_info (maskinfo_refined.txt) : Output file with mask filenames and rotational / translational operators + --psi (0.) : Third Euler angle (psi, in degrees) + --rot (0.) : First Euler angle (rot, in degrees) + --sphere_percentage (-1.) : Diameter of spherical mask divided by the box size (< 0.99) + --tilt (0.) : Second Euler angle (tilt, in degrees) + --xoff (0.) : X-offset (in Angstroms) + --yoff (0.) : Y-offset (in Angstroms) + --zoff (0.) : Z-offset (in Angstroms) + --verb (false) : Verbose output? + ====== Parameters (expert options - alphabetically ordered) ===== + --i_mask (mask.mrc) : (DEBUG) Input mask + --i_mask_info_parsed_ext (parsed) : Extension of parsed input file with mask filenames and rotational / translational operators + --use_healpix (false) : Use Healpix for angular samplings? + --width (5.) : Width of cosine soft edge (in pixels) + --version : Print RELION version and exit + +``relion_particle_subtract_mpi`` +--------------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Name of optimiser.star file from refinement/classification to use for subtraction + --o (Subtract/) : Output directory name + --mask () : Name of the 3D mask with all density that should be kept, i.e. not subtracted + --data () : Name of particle STAR file, in case not all particles from optimiser are to be used + --ignore_class (false) : Ignore the rlnClassNumber column in the particle STAR file. + --revert () : Name of particle STAR file to revert. When this is provided, all other options are ignored. + --ssnr (false) : Don't subtract, only calculate average spectral SNR in the images + ====== Centering options ===== + --recenter_on_mask (false) : Use this flag to center the subtracted particles on projections of the centre-of-mass of the input mask + --center_x (9999) : X-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --center_y (9999) : Y-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --center_z (9999) : Z-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --new_box (-1) : Output size of the subtracted particles + --version : Print RELION version and exit + +``relion_image_handler`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file, image (.mrc) or movie/stack (.mrcs) + --o () : Output name (for STAR-input: insert this string before each image's extension) + ====== image-by-constant operations ===== + --multiply_constant (1) : Multiply the image(s) pixel values by this constant + --divide_constant (1) : Divide the image(s) pixel values by this constant + --add_constant (0.) : Add this constant to the image(s) pixel values + --subtract_constant (0.) : Subtract this constant from the image(s) pixel values + --threshold_above (999.) : Set all values higher than this value to this value + --threshold_below (-999.) : Set all values lower than this value to this value + ====== image-by-image operations ===== + --multiply () : Multiply input image(s) by the pixel values in this image + --divide () : Divide input image(s) by the pixel values in this image + --add () : Add the pixel values in this image to the input image(s) + --subtract () : Subtract the pixel values in this image to the input image(s) + --fsc () : Calculate FSC curve of the input image with this image + --power (false) : Calculate power spectrum (|F|^2) of the input image + --adjust_power () : Adjust the power spectrum of the input image to be the same as this image + --fourier_filter () : Multiply the Fourier transform of the input image(s) with this one image + ====== additional subtract options ===== + --optimise_scale_subtract (false) : Optimise scale between maps before subtraction? + --optimise_bfactor_subtract (0.) : Search range for relative B-factor for subtraction (in A^2) + --mask_optimise_subtract () : Use only voxels in this mask to optimise scale for subtraction + ====== per-image operations ===== + --stats (false) : Calculate per-image statistics? + --com (false) : Calculate center of mass? + --bfactor (0.) : Apply a B-factor (in A^2) + --lowpass (-1.) : Low-pass filter frequency (in A) + --highpass (-1.) : High-pass filter frequency (in A) + --directional () : Directionality of low-pass filter frequency ('X', 'Y' or 'Z', default non-directional) + --LoG (-1.) : Diameter for optimal response of Laplacian of Gaussian filter (in A) + --angpix (-1) : Pixel size (in A) + --rescale_angpix (-1.) : Scale input image(s) to this new pixel size (in A) + --force_header_angpix (-1.) : Change the pixel size in the header (in A). Without --rescale_angpix, the image is not scaled. + --new_box (-1) : Resize the image(s) to this new box size (in pixel) + --filter_edge_width (2) : Width of the raised cosine on the low/high-pass filter edge (in resolution shells) + --flipX (false) : Flip (mirror) a 2D image or 3D map in the X-direction? + --flipY (false) : Flip (mirror) a 2D image or 3D map in the Y-direction? + --flipZ (false) : Flip (mirror) a 3D map in the Z-direction? + --invert_hand (false) : Invert hand by flipping X? Similar to flipX, but preserves the symmetry origin. Edge pixels are wrapped around. + --shift_com (false) : Shift image(s) to their center-of-mass (only on positive pixel values) + --shift_x (0.) : Shift images this many pixels in the X-direction + --shift_y (0.) : Shift images this many pixels in the Y-direction + --shift_z (0.) : Shift images this many pixels in the Z-direction + --avg_ampl (false) : Calculate average amplitude spectrum for all images? + --avg_ampl2 (false) : Calculate average amplitude spectrum for all images? + --avg_ampl2_ali (false) : Calculate average amplitude spectrum for all aligned images? + --average (false) : Calculate average of all images (without alignment) + --correct_avg_ampl () : Correct all images with this average amplitude spectrum + --minr_ampl_corr (0) : Minimum radius (in Fourier pixels) to apply average amplitudes + --remove_nan (false) : Replace non-numerical values (NaN, inf, etc) in the image(s) + --replace_nan (0) : Replace non-numerical values (NaN, inf, etc) with this value + --phase_randomise (-1) : Randomise phases beyond this resolution (in Angstroms) + ====== 3D operations ===== + --sym () : Symmetrise 3D map with this point group (e.g. D6) + ====== 2D-micrograph (or movie) operations ===== + --flipXY (false) : Flip the image(s) in the XY direction? + --flipmXY (false) : Flip the image(s) in the -XY direction? + --add_edge (false) : Add a barcode-like edge to the micrograph/movie frames? + --edge_x0 (0) : Pixel column to be used for the left edge + --edge_y0 (0) : Pixel row to be used for the top edge + --edge_xF (4095) : Pixel column to be used for the right edge + --edge_yF (4095) : Pixel row to be used for the bottom edge + ====== Movie-frame averaging options ===== + --avg_bin (-1) : Width (in frames) for binning average, i.e. of every so-many frames + --avg_first (-1) : First frame to include in averaging + --avg_last (-1) : Last frame to include in averaging + --average_all_movie_frames (false) : Average all movie frames of all movies in the input STAR file. + ====== PNG options ===== + --black (0) : Pixel value for black (default is auto-contrast) + --white (0) : Pixel value for white (default is auto-contrast) + --sigma_contrast (0) : Set white and black pixel values this many times the image stddev from the mean + --colour_fire (false) : Show images in black-grey-white-red colour scheme (highlight high signal)? + --colour_ice (false) : Show images in blue-black-grey-white colour scheme (highlight low signal)? + --colour_fire-n-ice (false) : Show images in blue-grey-red colour scheme (highlight high&low signal)? + --colour_rainbow (false) : Show images in cyan-blue-black-red-yellow colour scheme? + --colour_difference (false) : Show images in cyan-blue-black-red-yellow colour scheme (for difference images)? + --version : Print RELION version and exit + +``relion_motion_refine_mpi`` +----------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file + --o : Output directory, e.g. MotionFit/job041/ + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --first_frame (1) : First move frame to process + --last_frame (-1) : Last movie frame to process (default is all) + --only_do_unfinished (false) : Skip those steps for which output files already exist. + --verb (1) : Verbosity + ====== Motion fit options (basic) ===== + --fdose (-1) : Electron dose per frame (in e^-/A^2) + --s_vel (0.5) : Velocity sigma [Angst/dose] + --s_div (5000.0) : Divergence sigma [Angst] + --s_acc (2.0) : Acceleration sigma [Angst/dose] + --params_file () : File containing s_vel, s_div and s_acc (overrides command line parameters) + --only_group (-1) : Only align micrographs containing particles from this optics group (negative means off) + --diag (false) : Write out diagnostic data + ====== Motion fit options (advanced) ===== + --cc_pad (1.0) : Cross-correlation Fourier-padding + --dmg_a ( 3.40) : Damage model, parameter a + --dmg_b (-1.06) : b + --dmg_c (-0.54) : c + --max_iters (10000) : Maximum number of iterations + --eps (1e-5) : Terminate optimization after gradient length falls below this value + --no_whiten (false) : Do not whiten the noise spectrum + --unreg_glob (false) : Do not regularize global component of motion + --glob_off (false) : Compute initial per-particle offsets + --glob_off_max (10) : Maximum per-particle offset range [Pixels] + --absolute_params (false) : Do not scale input motion parameters by dose + --debug_opt (false) : Write optimization debugging info + --gi (false) : Initialize with global trajectories instead of loading them from metadata file + --sq_exp_ker (false) : Use a square-exponential kernel instead of an exponential one + --max_ed (-1) : Maximum number of eigendeformations + --out_cut (false) : Do not consider frequencies beyond the 0.143-FSC threshold for alignment + ====== Parameter estimation ===== + --params2 (false) : Estimate 2 parameters instead of motion + --params3 (false) : Estimate 3 parameters instead of motion + --align_frac (0.5) : Fraction of pixels to be used for alignment + --eval_frac (0.5) : Fraction of pixels to be used for evaluation + --min_p (1000) : Minimum number of particles on which to estimate the parameters + --par_group (-1) : Estimate parameters for this optics group only (negative means all) + --s_vel_0 (0.6) : Initial s_vel + --s_div_0 (10000) : Initial s_div + --s_acc_0 (3) : Initial s_acc + --in_step (3000) : Initial step size in s_div + --conv (30) : Abort when simplex diameter falls below this + --par_iters (100) : Max. number of iterations + --mot_range (50) : Limit allowed motion range [Px] + --seed (23) : Random seed for micrograph selection + ====== Combine frames options ===== + --combine_frames (false) : Combine movie frames into polished particles. + --scale (-1) : Re-scale the particles to this size (by default read from particles star file) + --window (-1) : Re-window the particles to this size (in movie-pixels; by default read from particles star file) + --crop (-1) : Crop the scaled particles to this size after CTF pre-multiplication + --ctf_multiply (false) : Premultiply by CTF. + --bfac_minfreq (20) : Min. frequency used in B-factor fit [Angst] + --bfac_maxfreq (-1) : Max. frequency used in B-factor fit [Angst] + --bfactors () : A .star file with external B/k-factors + --diag_bfactor (false) : Write out B/k-factor diagnostic data + --suffix () : Add this suffix to shiny MRCS and STAR files + --recenter (false) : Re-center particle according to rlnOriginX/Y in --reextract_data_star STAR file + --recenter_x (0.) : X-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_y (0.) : Y-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_z (0.) : Z-coordinate (in pixel inside the reference) to recenter re-extracted data on + ====== Computational options ===== + --j (1) : Number of (OMP) threads + --min_MG (0) : First micrograph index + --max_MG (-1) : Last micrograph index (default is to process all) + --sbs (false) : Load movies slice-by-slice to save memory (slower) + ====== Expert options ===== + --corr_mic : List of uncorrected micrographs (e.g. corrected_micrographs.star) + --find_shortest (false) : Load only as many frames as are present in all movies. + --debug (false) : Write debugging data + --mps (-1) : Pixel size of input movies (Angst/pix) + --cps (-1) : Pixel size of particle coordinates in star-file (Angst/pix) + --hot (-1) : Clip hot pixels to this max. value (-1 = off, TIFF only) + --debug_mov (false) : Write debugging data for movie loading + --mov_toReplace () : Replace this string in micrograph names... + --mov_replaceBy () : ..by this one + --eer_upsampling (-1) : EER upsampling (1 = 4K or 2 = 8K) + --eer_grouping (-1) : EER grouping + --version : Print RELION version and exit + +``relion_project`` +------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i : Input map to be projected + --o (proj) : Rootname for output projections + --ctf (false) : Apply CTF to reference projections + --ctf_phase_flip (false) : Flip phases of the CTF in the output projections + --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? + --angpix (-1) : Pixel size (in Angstroms) + --mask () : Mask that will be applied to the input map prior to making projections + --ang (None) : Particle STAR file with orientations and CTF for multiple projections (if None, assume single projection) + --nr_uniform (-1) : OR get this many random samples from a uniform angular distribution + --sigma_offset (0) : Apply Gaussian errors with this stddev to the XY-offsets + --rot (0) : First Euler angle (for a single projection) + --tilt (0) : Second Euler angle (for a single projection) + --psi (0) : Third Euler angle (for a single projection) + --xoff (0) : Origin X-offsets (in pixels) (for a single projection) + --yoff (0) : Origin Y-offsets (in pixels) (for a single projection) + --zoff (0) : Origin Z-offsets (in pixels) (for a single 3D rotation) + --add_noise (false) : Add noise to the output projections (only with --ang) + --white_noise (0) : Standard deviation of added white Gaussian noise + --model_noise () : Model STAR file with power spectra for coloured Gaussian noise + --subtract_exp (false) : Subtract projections from experimental images (in --ang) + --ignore_particle_name (false) : Ignore the rlnParticleName column (in --ang) + --3d_rot (false) : Perform 3D rotations instead of projection into 2D images + --simulate (false) : Simulate data with known ground-truth by subtracting signal and adding projection in random orientation. + --adjust_simulation_SNR (1.) : Relative SNR compared to input images for realistic simulation of data + --ang_simulate () : STAR file with orientations for projections of realistic simulations (random from --ang STAR file by default) + --maxres (-1) : Maximum resolution (in Angstrom) to consider in Fourier space (default Nyquist) + --pad (2) : Padding factor + --ctf2 (false) : Apply CTF*CTF to reference projections + --NN (false) : Use nearest-neighbour instead of linear interpolation + --version : Print RELION version and exit + +``relion_star_datablock_stack`` +-------------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_datablock_stack ... + + === Purpose: === + This (bash) script generates the datablock for N images in a stack named stackname + Other (optional) data values are in value1, value2, etc. + + === Example: === + /relion_star_datablock_stack 3 my_images.mrcs 10000 10500 0.0 200 2 0.1 + yields: + 000001@my_images.mrcs 10000 10500 0.0 200 2 0.1 + 000002@my_images.mrcs 10000 10500 0.0 200 2 0.1 + 000003@my_images.mrcs 10000 10500 0.0 200 2 0.1 + +``relion_ctf_refine_mpi`` +-------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file containing the particles + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --o : Output directory, e.g. CtfRefine/job041/ + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --only_do_unfinished (false) : Skip those steps for which output files already exist. + --ctf_pad (false) : Use larger box to calculate CTF and then downscale to mimic boxing operation in real space + --diag (false) : Write out diagnostic data (slower) + ====== Defocus fit options ===== + --fit_defocus (false) : Perform refinement of per-particle defocus values? + --fit_mode (fpmfm) : String of 5 characters describing whether to fit the phase shift (1), + defocus (2), astigmatism (3), spherical aberration (4) and B-factors (5) + per particle ('p'), per micrograph ('m') or to keep them fixed ('f') + during the per-micrograph CTF refinement. + --max_defocus_iters (100) : Maximum number of iterations for CTF refinement. + --bf0 (false) : Perform brute-force per-particle defocus search (as in RELION 3.0) prior + to the per-micrograph CTF refinement. + --bf1 (false) : Perform brute-force defocus search after CTF refinement. + --bf_only (false) : Skip CTF refinement and only perform a brute-force defocus search. + --bf_range (2000.) : Defocus scan range (in A) for brute-force search. + --legacy_astig (false) : Estimate independent per-particle astigmatism (from RELION 3.0) + --kmin_defocus (30.0) : Inner freq. threshold for defocus estimation [Angst] + ====== B-factor options ===== + --fit_bfacs (false) : Estimate CTF B-factors + --bfac_per_mg (false) : Estimate B-factors per micrograph, instead of per particle + --bfac_min_B (-30) : Minimal allowed B-factor + --bfac_max_B (300) : Maximal allowed B-factor + --bfac_min_scale (0.2) : Minimal allowed scale-factor (essential for outlier rejection) + --kmin_bfac (30.0) : Inner freq. threshold for B-factor estimation [Angst] + ====== Beam-tilt options ===== + --fit_beamtilt (false) : Perform refinement of beamtilt + --kmin_tilt (20.0) : Inner freq. threshold for beamtilt estimation [Å] + --odd_aberr_max_n (0) : Maximum degree of Zernike polynomials used to fit odd (i.e. antisymmetrical) aberrations + --xr0_t (-1) : Exclusion ring start [Å] - use to exclude dominant frequency (e.g. for helices) + --xr1_t (-1) : Exclusion ring end [Å] + ====== Symmetric aberrations options ===== + --fit_aberr (false) : Estimate symmetric aberrations + --kmin_aberr (20.0) : Inner freq. threshold for symmetrical aberration estimation [Å] + --even_aberr_max_n (4) : Maximum degree of Zernike polynomials used to fit even (i.e. symmetrical) aberrations + --xr0_a (-1) : Exclusion ring start [Å] + --xr1_a (-1) : Exclusion ring end [Å] + ====== Anisotropic magnification options ===== + --fit_aniso (false) : Estimate anisotropic magnification + --kmin_mag (20.0) : Inner freq. threshold for anisotropic magnification estimation [Angst] + --keep_astig (false) : Do not translate astigmatism into new coordinates + --part_astig (false) : Allow astigmatism to vary among the particles of a micrograph + ====== Computational options ===== + --j (1) : Number of (OMP) threads + --min_MG (0) : First micrograph index + --max_MG (-1) : Last micrograph index (default is to process all) + --debug (false) : Write debugging data + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_plot_delocalisation`` +------------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input particle *.star file + --rad : Particle radius [Å] + --o : Output path + --og (1) : Optics group + --max_freq (-1) : Max. image frequency [Å] (default is Nyquist) + --min_freq (0) : Min. image frequency [Å] + --name () : Name of dataset (for the plot) + --all_part (false) : Consider all particles, instead of only the first one in each micrograph + --s (256) : Square size for estimation + --j (1) : Number of threads + --version : Print RELION version and exit + +``relion_star_plottable`` +-------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_plottable + + === Purpose: === + This (bash) script uses gnuplot to plot content from a datablock (with name ) in + It will make a plot of the values given for against those of + If is not given, the values of will be plotted linearly + + === Example: === + /relion_star_plottable run3_it024_model.star run3_it024_model.star data_model_class_1 rlnSsnrMap rlnResolution + +``relion_reconstruct_mpi`` +--------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Input STAR file with the projection images and their orientations + --o (relion.mrc) : Name for output reconstruction + --sym (c1) : Symmetry group + --maxres (-1) : Maximum resolution (in Angstrom) to consider in Fourier space (default Nyquist) + --pad (2) : Padding factor + --img () : Optional: image path prefix + --subset (-1) : Subset of images to consider (1: only reconstruct half1; 2: only half2; other: reconstruct all) + --class (-1) : Consider only this class (-1: use all classes) + --angpix (-1) : Pixel size in the reconstruction (take from first optics group by default) + ====== CTF options ===== + --ctf (false) : Apply CTF correction + --ctf_intact_first_peak (false) : Leave CTFs intact until first peak + --ctf_phase_flipped (false) : Images have been phase flipped + --only_flip_phases (false) : Do not correct CTF-amplitudes, only flip phases + ====== Ewald-sphere correction options ===== + --ewald (false) : Correct for Ewald-sphere curvature (developmental) + --mask_diameter (-1.) : Diameter (in A) of mask for Ewald-sphere curvature correction + --width_mask_edge (3) : Width (in pixels) of the soft edge on the mask + --reverse_curvature (false) : Try curvature the other way around + --newbox (-1) : Box size of reconstruction after Ewald sphere correction + --sectors (2) : Number of sectors for Ewald sphere correction + --skip_mask (false) : Do not apply real space mask during Ewald sphere correction + --skip_weighting (false) : Do not apply weighting during Ewald sphere correction + ====== Helical options ===== + --nr_helical_asu (1) : Number of helical asymmetrical units + --helical_rise (0.) : Helical rise (in Angstroms) + --helical_twist (0.) : Helical twist (in degrees, + for right-handedness) + ====== Expert options ===== + --subtract () : Subtract projections of this map from the images used for reconstruction + --NN (false) : Use nearest-neighbour instead of linear interpolation before gridding correction + --blob_r (1.9) : Radius of blob for gridding interpolation + --blob_m (0) : Order of blob for gridding interpolation + --blob_a (15) : Alpha-value of blob for gridding interpolation + --iter (10) : Number of gridding-correction iterations + --refdim (3) : Dimension of the reconstruction (2D or 3D) + --angular_error (0.) : Apply random deviations with this standard deviation (in degrees) to each of the 3 Euler angles + --shift_error (0.) : Apply random deviations with this standard deviation (in Angstrom) to each of the 2 translations + --fom_weighting (false) : Weight particles according to their figure-of-merit (_rlnParticleFigureOfMerit) + --fsc () : FSC-curve for regularized reconstruction + --3d_rot (false) : Perform 3D rotations instead of backprojections from 2D images + --reconstruct_ctf (-1) : Perform a 3D reconstruction from 2D CTF-images, with the given size in pixels + --ctf2 (false) : Reconstruct CTF^2 and then take the sqrt of that + --skip_gridding (false) : Skip gridding part of the reconstruction + --debug () : Rootname for debug reconstruction files + --debug_ori_size (1) : Rootname for debug reconstruction files + --debug_size (1) : Rootname for debug reconstruction files + --reconstruct_noise () : Reconstruct noise using sigma2 values in this model STAR file + --read_weights (false) : Developmental: read freq. weight files + --write_debug_output (false) : Write out arrays with data and weight terms prior to reconstruct + --external_reconstruct (false) : Write out BP denominator and numerator for external_reconstruct program + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_ctf_toolbox`` +----------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Pre-multiply options ===== + --i () : Input STAR file with CTF information + --o () : Output rootname (for multiple images: insert this string before each image's extension) + ====== OR: simulate options ===== + --simulate () : Output name for simulated CTF image + --angpix (1.) : Pixel size (A) + --box (256) : Box size (pix) + --kV (300) : Voltage (kV) + --Q0 (0.1) : Amplitude contrast + --Cs (2.7) : Spherical aberration (mm) + --defU (20000) : Defocus in U-direction (A) + --defV (-1.) : Defocus in V-direction (A, default = defU) + --defAng (0.) : Defocus angle (deg) + --phase_shift (0.) : Phase shift (deg) + ====== Shared options ===== + --ctf_intact_first_peak (false) : Leave CTFs intact until first peak + --ctf_intact_after_first_peak (false) : Leave CTFs intact after first peak + --ctf_pad (false) : Pre-multiply with a 2x finer-sampled CTF that is then downscaled + --version : Print RELION version and exit + +``relion_stack_create`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file with the images (as rlnImageName) to be saved in a stack + --o (output) : Output rootname + --spider_format (false) : Write out in SPIDER stack format (by default MRC stack format) + --split_per_micrograph (false) : Write out separate stacks for each micrograph (needs rlnMicrographName in STAR file) + --apply_transformation (false) : Apply the inplane-transformations (needs _rlnOriginX/Y and _rlnAnglePsi in STAR file) by real space interpolation + --apply_rounded_offsets_only (false) : Apply the rounded translations only (so-recentering without interpolation; needs _rlnOriginX/Y in STAR file) + --ignore_optics (false) : Ignore optics groups. This allows you to read and write RELION 3.0 STAR files but does NOT allow you to convert 3.1 STAR files back to the 3.0 format. + --one_by_one (false) : Write particles one by one. This saves memory but can be slower. + --version : Print RELION version and exit + +``relion_external_reconstruct`` +-------------------------------------------------------------------------- + +.. code-block:: text + + ERROR: + Usage: relion_external_reconstruct input.star + === Backtrace === + relion_external_reconstruct(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x7d) [0x561b0d91604d] + relion_external_reconstruct(_ZN21ext_recons_parameters4readEiPPc+0x120b) [0x561b0d8eb8bb] + relion_external_reconstruct(main+0x45) [0x561b0d8e1645] + /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f332f717d90] + /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f332f717e40] + relion_external_reconstruct(_start+0x25) [0x561b0d8e1ca5] + ================== + ERROR: + Usage: relion_external_reconstruct input.star + +``relion_tomo_test`` +--------------------------------------------------------------- + +.. code-block:: text + + reading: frames/bin4_0.mrc + +``relion_flex_analyse`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --data () : The _data.star file with the orientations to be analysed + --model () : The corresponding _model.star file with the refined model + --bodies () : The corresponding star file with the definition of the bodies + --o (analyse) : Output rootname + ====== 3D model options ===== + --3dmodels (false) : Generate a 3D model for each experimental particles + --size_3dmodels (-1) : Output size of the 3D models (default is same as input particles) + ====== PCA options ===== + --PCA_orient (false) : Perform a principal components analysis on the multibody orientations + --do_maps (false) : Generate maps along the principal components + --k (-1) : Number of principal components to generate maps for + --v (0.75) : Or use as many principal components to explain this fraction of variance (<0,1]) + --maps_per_movie (10) : Number of maps to use for the movie of each principal component + --bins (100) : Number of bins in histograms of the eigenvalues for each principal component + --select_eigenvalue (-1) : Output a selection particle.star file based on eigenvalues along this eigenvector + --select_eigenvalue_min (-99999.) : Minimum for eigenvalue to include particles in selection output star file + --select_eigenvalue_max (99999.) : Maximum for eigenvalue to include particles in selection output star file + --write_pca_projections (false) : Write out a text file with all PCA projections for all particles + --verb (1) : Verbosity + --version : Print RELION version and exit + +``relion_refine_mpi`` +---------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Input images (in a star-file) + --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) + --K (1) : Number of references to be refined + --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) + --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) + --flatten_solvent (false) : Perform masking on the references as well? + --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) + --solvent_mask2 (None) : User-provided secondary mask (with its own average density) + --lowpass_mask (None) : User-provided mask for low-pass filtering + --lowpass (0) : User-provided cutoff for region specified above + --tau (None) : STAR file with input tau2-spectrum (to be kept constant) + --local_symmetry (None) : Local symmetry description file containing list of masks and their operators + --split_random_halves (false) : Refine two random halves of the data completely separately + --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations + ====== Initialisation ===== + --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) + --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles + --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) + --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) + --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration + ====== Orientations ===== + --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) + --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc + --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) + --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views + --sym (c1) : Symmetry group + --relax_sym () : Symmetry to be relaxed + --offset_range (6) : Search range for origin offsets (in pixels) + --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) + --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (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) + --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) + --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) + --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) + --skip_align (false) : Skip orientational assignment (only classify)? + --skip_rotate (false) : Skip rotational assignment (only translate and classify)? + --bimodal_psi (false) : Do bimodal searches of psi angle? + ====== Helical reconstruction (in development...) ===== + --helix (false) : Perform 3D classification or refinement for helices? + --ignore_helical_symmetry (false) : Ignore helical symmetry? + --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) + --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) + --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) + --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) + --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) + --helical_rise_initial (0.) : Helical rise (in Angstroms) + --helical_rise_min (0.) : Minimum helical rise (in Angstroms) + --helical_rise_max (0.) : Maximum helical rise (in Angstroms) + --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) + --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) + --helical_z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix. Important in imposing and refining symmetry + --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) + --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) + --helical_symmetry_search (false) : Perform local refinement of helical symmetry? + --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks + --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? + --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) + --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector + ====== Corrections ===== + --ctf (false) : Perform CTF correction? + --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? + --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? + --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? + --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? + --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) + --norm (false) : Perform normalisation-error correction? + --scale (false) : Perform intensity-scale corrections on image groups? + --no_norm (false) : Switch off normalisation-error correction? + --no_scale (false) : Switch off intensity-scale corrections on image groups? + ====== Stochastic Gradient Descent ===== + --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization + --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users + --sgd_ini_iter (50) : Number of initial SGD iterations + --sgd_fin_iter (50) : Number of final SGD iterations + --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones + --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) + --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) + --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations + --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations + --mu (0.9) : Momentum parameter for SGD updates + --sgd_stepsize (0.5) : Step size parameter for SGD updates + --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) + --sgd_sigma2fudge_halflife (-1) : Initialise SGD with 8x higher noise-variance, and reduce with this half-life in # of particles (default is keep normal variance) + --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off + --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) + ====== Computation ===== + --pool (1) : Number of images to pool for each thread task + --j (1) : Number of threads to run in parallel (only useful on multi-core machines) + --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc + --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory + --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) + --preread_images (false) : Use this to let the leader process read all particles into memory. Be careful you have enough RAM for large data sets! + --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. + --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) + --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. + --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. + --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations + --gpu (false) : Use available gpu resources for some calculations + --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. + ====== Expert options ===== + --pad (2) : Oversampling factor for the Fourier transforms of the references + --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) + --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? + --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation + --verb (1) : Verbosity (1=normal, 0=silent) + --random_seed (-1) : Number for the random seed generator + --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach + --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling + --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) + --fix_sigma_noise (false) : Fix the experimental noise spectra? + --fix_sigma_offset (false) : Fix the stddev in the origin offsets? + --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement + --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit + --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit + --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step + --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step + --dont_check_norm (false) : Skip the check whether the images are normalised correctly + --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) + --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? + --skip_maximize (false) : Skip maximization step (only write out data.star file)? + --failsafe_threshold (40) : Maximum number of particles permitted to be handled by fail-safe mode, due to zero sum of weights, before exiting with an error (GPU only). + --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) + --auto_iter_max (999) : In auto-refinement, stop at this iteration. + --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. + --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. + --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. + --trust_ref_size (false) : Trust the pixel and box size of the input reference; by default the program will die if these are different from the first optics group of the data + --maxsig (-1) : Maximum number of poses & translations to consider + --skip_gridding (false) : Skip gridding in the M step + ====== MPI options ===== + --halt_all_followers_except (-1) : For debugging: keep all followers except this one waiting + --keep_debug_reconstruct_files (false) : For debugging: keep temporary data and weight files for debug-reconstructions. + --version : Print RELION version and exit + +``relion_star_handler`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file + --o (out.star) : Output STAR file + --ignore_optics (false) : Provide this option for relion-3.0 functionality, without optics groups + --angpix (1.) : Pixel size in Angstrom, for when ignoring the optics groups in the input star file + --i_tablename () : If ignoring optics, then read table with this name + ====== Compare options ===== + --compare () : STAR file name to compare the input STAR file with + --label1 () : 1st metadata label for the comparison (may be string, int or RFLOAT) + --label2 () : 2nd metadata label for the comparison (RFLOAT only) for 2D/3D-distance) + --label3 () : 3rd metadata label for the comparison (RFLOAT only) for 3D-distance) + --max_dist (0.) : Maximum distance to consider a match (for int and RFLOAT only) + ====== Select options ===== + --select () : Metadata label (number) to base output selection on (e.g. rlnCtfFigureOfMerit) + --minval (-99999999.) : Minimum acceptable value for this label (inclusive) + --maxval (99999999.) : Maximum acceptable value for this label (inclusive) + --select_by_str () : Metadata label (string) to base output selection on (e.g. rlnMicrographname) + --select_include () : select rows that contains this string in --select_by_str + --select_exclude () : exclude rows that contains this string in --select_by_str + ====== Discard based on image statistics options ===== + --discard_on_stats (false) : Discard images if their average/stddev deviates too many sigma from the ensemble average + --discard_label (rlnImageName) : MetaDataLabel that points to the images to be used for discarding based on statistics + --discard_sigma (4.) : Discard images with average or stddev values that lie this many sigma away from the ensemble average + ====== Combine options ===== + --combine (false) : Combine input STAR files (multiple individual filenames, all within double-quotes after --i) + --check_duplicates () : MetaDataLabel (for a string only!) to check for duplicates, e.g. rlnImageName + ====== Split options ===== + --split (false) : Split the input STAR file into one or more smaller output STAR files + --random_order (false) : Perform splits on randomised order of the input STAR file + --random_seed (-1) : Random seed for randomisation. + --nr_split (-1) : Split into this many equal-sized STAR files + --size_split (-1) : AND/OR split into subsets of this many lines + ====== Operate options ===== + --operate () : Operate on this metadata label + --operate2 () : Operate also on this metadata label + --operate3 () : Operate also on this metadata label + --set_to () : Set all the values for the --operate label(s) to this value + --multiply_by (1.) : Multiply all the values for the --operate label(s) by this value + --add_to (0.) : Add this value to all the values for the --operate label(s) + ====== Center options ===== + --center (false) : Perform centering of particles according to a position in the reference. + --center_X (0.) : X-coordinate in the reference to center particles on (in pix) + --center_Y (0.) : Y-coordinate in the reference to center particles on (in pix) + --center_Z (0.) : Z-coordinate in the reference to center particles on (in pix) + ====== Column options ===== + --remove_column () : Remove the column with this metadata label from the input STAR file. + --add_column () : Add a column with this metadata label from the input STAR file. + --add_column_value () : Set this value in all rows for the added column + --copy_column_from () : Copy values in this column to the added column + --hist_column () : Calculate histogram of values in the column with this metadata label + --in_percent (false) : Show a histogram in percent (need --hist_column) + --show_cumulative (false) : Show a histogram of cumulative distribution (need --hist_column) + --hist_bins (-1) : Number of bins for the histogram. By default, determined automatically by Freedman–Diaconis rule. + --hist_min (-inf) : Minimum value for the histogram (needs --hist_bins) + --hist_max (inf) : Maximum value for the histogram (needs --hist_bins) + ====== Duplicate removal ===== + --remove_duplicates (-1) : Remove duplicated particles within this distance [Angstrom]. Negative values disable this. + --image_angpix (-1) : For down-sampled particles, specify the pixel size [A/pix] of the original images used in the Extract job + --version : Print RELION version and exit + +``relion_star_datablock_singlefiles`` +-------------------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_datablock_singlefiles "*.spi" ... + + === Purpose: === + This (bash) script generates the datablock for all images represented by the wildcard in the first argument + Other (optional) data values are in value1, value2, etc. + + === Example: === + /relion_star_datablock_singlefiles "tmp/*" 10000 10500 0.0 200 2 0.1 + yields: + tmp/t1.spi 10000 10500 0.0 200 2 0.1 + tmp/t2.spi 10000 10500 0.0 200 2 0.1 + tmp/t3.spi 10000 10500 0.0 200 2 0.1 + +``relion_qsub`` +-------------------------------------------------------------- + +.. code-block:: text + + /bin/sh: 1: relion_qsub.csh: not found + +``relion_align_symmetry`` +-------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i : Input map to be projected + --sym : Target point group symmetry + --o (aligned.mrc) : Rootname for output projections + --box_size (64) : Working box size in pixels. Very small box (such that Nyquist is aroud 20 A) is usually sufficient. + --keep_centre (false) : Do not re-centre the input + --angpix (-1) : Pixel size (in Angstroms) + --only_rot (false) : Keep TILT and PSI fixed and search only ROT (rotation along the Z axis) + --nr_uniform (400) : Randomly search this many orientations + --maxres (-1) : Maximum resolution (in Angstrom) to consider in Fourier space (default Nyquist) + --local_search_range (2) : Local search range (1 + 2 * this number) + --local_search_step (2) : Local search step (in degrees) + --pad (2) : Padding factor + --NN (false) : Use nearest-neighbour instead of linear interpolation + --version : Print RELION version and exit + +``relion_autopick`` +-------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Micrograph STAR file OR filenames from which to autopick particles, e.g. "Micrographs/*.mrc" + --pickname (autopick) : Rootname for coordinate STAR files + --odir (AutoPick/) : Output directory for coordinate files (default is to store next to micrographs) + --angpix (1) : Pixel size of the micrographs in Angstroms + --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms, default=automatic) + --shrink_particle_mask (2) : Shrink the particle mask by this many pixels (to detect Einstein-from-noise classes) + --outlier_removal_zscore (8.) : Remove pixels that are this many sigma away from the mean + --write_fom_maps (false) : Write calculated probability-ratio maps to disc (for re-reading in subsequent runs) + --no_fom_limit (false) : Ignore default maximum limit of 30 fom maps being written + --read_fom_maps (false) : Skip probability calculations, re-read precalculated maps from disc + --skip_optimise_scale (false) : Skip the optimisation of the micrograph scale for better prime factors in the FFTs. This runs slower, but at exactly the requested resolution. + --only_do_unfinished (false) : Only autopick those micrographs for which the coordinate file does not yet exist + --gpu (false) : Use GPU acceleration when availiable + ====== References options ===== + --ref () : STAR file with the reference names, or an MRC stack with all references, or "gauss" for blob-picking + --angpix_ref (-1) : Pixel size of the references in Angstroms (default is same as micrographs) + --invert (false) : Density in micrograph is inverted w.r.t. density in template + --ang (10) : Angular sampling (in degrees); use 360 for no rotations + --lowpass (-1) : Lowpass filter in Angstroms for the references (prevent Einstein-from-noise!) + --highpass (-1) : Highpass filter in Angstroms for the micrographs + --ctf (false) : Perform CTF correction on the references? + --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? + --gauss_max (0.1) : Value of the peak in the Gaussian blob reference + --healpix_order (1) : Healpix order for projecting a 3D reference (hp0=60deg; hp1=30deg; hp2=15deg) + --sym (C1) : Symmetry point group for a 3D reference + ====== Laplacian-of-Gaussian options ===== + --LoG (false) : Use Laplacian-of-Gaussian filter-based picking, instead of template matching + --LoG_diam_min (-1) : Smallest particle diameter (in Angstroms) for blob-detection by Laplacian-of-Gaussian filter + --LoG_diam_max (-1) : Largest particle diameter (in Angstroms) for blob-detection by Laplacian-of-Gaussian filter + --LoG_neighbour (100) : Avoid neighbouring particles within (the detected diameter + the minimum diameter) times this percent + --Log_invert (false) : Use this option if the particles are white instead of black + --LoG_adjust_threshold (0.) : Use this option to adjust the picking threshold: positive for less particles, negative for more + --LoG_upper_threshold (99999) : Use this option to set the upper limit of the picking threshold + --LoG_use_ctf (false) : Use CTF until the first peak in Laplacian-of-Gaussian picker + ====== Helix options ===== + --helix (false) : Are the references 2D helical segments? If so, in-plane rotation angles (psi) are estimated for the references. + --helical_tube_kappa_max (0.25) : Factor of maximum curvature relative to that of a circle + --helical_tube_outer_diameter (-1) : Tube diameter in Angstroms + --helical_tube_length_min (-1) : Minimum tube length in Angstroms + --amyloid (false) : Activate specific algorithm for amyloid picking? + ----max_diam_local_avg (-1) : Maximum diameter to calculate local average density in Angstroms + ====== Peak-search options ===== + --threshold (0.25) : Fraction of expected probability ratio in order to consider peaks? + --min_distance (-1) : Minimum distance (in A) between any two particles (default is half the box size) + --max_stddev_noise (-1) : Maximum standard deviation in the noise area to use for picking peaks (default is no maximum) + --min_avg_noise (-999.) : Minimum average in the noise area to use for picking peaks (default is no minimum) + --skip_side (0) : Keep this many extra pixels (apart from particle_size/2) away from the edge of the micrograph + ====== Expert options ===== + --verb (1) : Verbosity + --pad (2) : Padding factor for Fourier transforms + --random_seed (1) : Number for the random seed generator + --shrink (1.0) : Reduce micrograph to this fraction size, during correlation calc (saves memory and time) + --Log_max_search (5.) : Maximum diameter in LoG-picking multi-scale approach is this many times the min/max diameter + --extra_pad (0) : Number of pixels for additional padding of the original micrograph + --version : Print RELION version and exit + +``relion_particle_subtract`` +----------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : Name of optimiser.star file from refinement/classification to use for subtraction + --o (Subtract/) : Output directory name + --mask () : Name of the 3D mask with all density that should be kept, i.e. not subtracted + --data () : Name of particle STAR file, in case not all particles from optimiser are to be used + --ignore_class (false) : Ignore the rlnClassNumber column in the particle STAR file. + --revert () : Name of particle STAR file to revert. When this is provided, all other options are ignored. + --ssnr (false) : Don't subtract, only calculate average spectral SNR in the images + ====== Centering options ===== + --recenter_on_mask (false) : Use this flag to center the subtracted particles on projections of the centre-of-mass of the input mask + --center_x (9999) : X-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --center_y (9999) : Y-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --center_z (9999) : Z-coordinate of 3D coordinate, which will be projected to center the subtracted particles. + --new_box (-1) : Output size of the subtracted particles + --version : Print RELION version and exit + +``relion_particle_symmetry_expand`` +------------------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i : Input particle STAR file + --o (expanded.star) : Output expanded particle STAR file + --sym (C1) : Symmetry point group + ====== Helix ===== + --helix (false) : Do helical symmetry expansion + --twist (0.) : Helical twist (deg) + --rise (0.) : Helical rise (A) + --angpix (1.) : Pixel size (A) + --asu (1) : Number of asymmetrical units to expand + --frac_sampling (1) : Number of samplings in between a single asymmetrical unit + --frac_range (0.5) : Range of the rise [-0.5, 0.5> to be sampled + --ignore_optics (false) : Provide this option for relion-3.0 functionality, without optics groups + --version : Print RELION version and exit + +``relion_localsym`` +-------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Show usage ===== + --function_help (false) : Show usage for the selected function (JUN 30, 2017) + ====== Options ===== + --apply (false) : Apply local symmetry to a 3D cryo-EM density map + --duplicate (false) : Duplicate subunits/masks according to local symmetry operators + --search (false) : Local searches of local symmetry operators + --transform (false) : Transform a map according to three Euler angles and XYZ translations + --txt2rln (false) : Convert operators from DM to RELION STAR format + --debug (false) : (DEBUG ONLY) + ====== Parameters (alphabetically ordered) ===== + --angpix (1.) : Pixel size (in Angstroms) of input image + --ang_range (0.) : Angular search range of operators (in degrees), overwrite rot-tilt-psi ranges if set to positive + --ang_rot_range (0.) : Angular (rot) search range of operators (in degrees) + --ang_tilt_range (0.) : Angular (tilt) search range of operators (in degrees) + --ang_psi_range (0.) : Angular (psi) search range of operators (in degrees) + --ang_step (1.) : Angular search step of operators (in degrees) + --bin (-1.) : Binning factor (<= 1 means no binning) + --ini_threshold (0.01) : Initial threshold for binarization + --i_map () : Input 3D unsymmetrised map + --i_mask_info (maskinfo.txt) : Input file with mask filenames and rotational / translational operators (for local searches) + --i_op_mask_info (None) : Input file with mask filenames for all operators (for global searches) + --n (2) : Create this number of masks according to the input density map + --offset_range (0.) : Translational search range of operators (in Angstroms), overwrite x-y-z ranges if set to positive + --offset_x_range (0.) : Translational (x) search range of operators (in Angstroms) + --offset_y_range (0.) : Translational (y) search range of operators (in Angstroms) + --offset_z_range (0.) : Translational (z) search range of operators (in Angstroms) + --offset_step (1.) : Translational search step of operators (in Angstroms) + --o_map () : Output 3D symmetrised map + --o_mask_info (maskinfo_refined.txt) : Output file with mask filenames and rotational / translational operators + --psi (0.) : Third Euler angle (psi, in degrees) + --rot (0.) : First Euler angle (rot, in degrees) + --sphere_percentage (-1.) : Diameter of spherical mask divided by the box size (< 0.99) + --tilt (0.) : Second Euler angle (tilt, in degrees) + --xoff (0.) : X-offset (in Angstroms) + --yoff (0.) : Y-offset (in Angstroms) + --zoff (0.) : Z-offset (in Angstroms) + --verb (false) : Verbose output? + ====== Parameters (expert options - alphabetically ordered) ===== + --i_mask (mask.mrc) : (DEBUG) Input mask + --i_mask_info_parsed_ext (parsed) : Extension of parsed input file with mask filenames and rotational / translational operators + --use_healpix (false) : Use Healpix for angular samplings? + --width (5.) : Width of cosine soft edge (in pixels) + --version : Print RELION version and exit + +``relion_preprocess`` +---------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i () : The STAR file with all (selected) micrographs to extract particles from + --coord_suffix () : The suffix for the coordinate files, e.g. "_picked.star" or ".box" + --coord_dir (ASINPUT) : The directory where the coordinate files are (default is same as micrographs) + --part_dir (Particles/) : Output directory for particle stacks + --part_star () : Output STAR file with all particles metadata + --reextract_data_star () : A _data.star file from a refinement to re-extract, e.g. with different binning or re-centered (instead of --coord_suffix) + --keep_ctfs_micrographs (false) : By default, CTFs from fn_data will be kept. Use this flag to keep CTFs from input micrographs STAR file + --reset_offsets (false) : reset the origin offsets from the input _data.star file to zero? + --recenter (false) : Re-center particle according to rlnOriginX/Y in --reextract_data_star STAR file + --recenter_x (0.) : X-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_y (0.) : Y-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_z (0.) : Z-coordinate (in pixel inside the reference) to recenter re-extracted data on + --ref_angpix (-1) : Pixel size of the reference used for recentering. -1 uses the pixel size of particles. + ====== Particle extraction ===== + --extract (false) : Extract all particles from the micrographs + --extract_size (-1) : Size of the box to extract the particles in (in pixels) + --premultiply_ctf (false) : Premultiply the micrograph/frame with its CTF prior to particle extraction + --premultiply_extract_size (-1) : Size of the box to extract the particles in (in pixels) before CTF premultiplication + --ctf_intact_first_peak (false) : When premultiplying with the CTF, leave frequencies intact until the first peak + --phase_flip (false) : Flip CTF-phases in the micrograph/frame prior to particle extraction + --extract_bias_x (0) : Bias in X-direction of picked particles (this value in pixels will be added to the coords) + --extract_bias_y (0) : Bias in Y-direction of picked particles (this value in pixels will be added to the coords) + --only_do_unfinished (false) : Extract only particles if the STAR file for that micrograph does not yet exist. + ====== Particle operations ===== + --project3d (false) : Project sub-tomograms along Z to generate 2D particles + --scale (-1) : Re-scale the particles to this size (in pixels) + --window (-1) : Re-window the particles to this size (in pixels) + --norm (false) : Normalise the background to average zero and stddev one + --no_ramp (false) : Just subtract the background mean in the normalisation, instead of subtracting a fitted ramping background. + --bg_radius (-1) : Radius of the circular mask that will be used to define the background area (in pixels) + --white_dust (-1) : Sigma-values above which white dust will be removed (negative value means no dust removal) + --black_dust (-1) : Sigma-values above which black dust will be removed (negative value means no dust removal) + --invert_contrast (false) : Invert the contrast in the input images + --operate_on () : Use this option to operate on an input image stack + --operate_out (preprocessed.mrcs) : Output name when operating on an input image stack + ====== Helix extraction ===== + --helix (false) : Extract helical segments + --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical segments) + --helical_tubes (false) : Extract helical segments from tube coordinates + --helical_nr_asu (1) : Number of helical asymmetrical units + --helical_rise (0.) : Helical rise (in Angstroms) + --helical_bimodal_angular_priors (false) : Add bimodal angular priors for helical segments + --helical_cut_into_segments (false) : Cut helical tubes into segments + --version : Print RELION version and exit + +``relion_run_motioncorr_mpi`` +------------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : STAR file with all input micrographs, or a Linux wildcard with all micrographs to operate on + --o (MotionCorr) : Name for the output directory + --j (1) : Number of threads per movie (= process) + --max_io_threads (-1) : Limit the number of IO threads. + --only_do_unfinished (false) : Only run motion correction for those micrographs for which there is not yet an output micrograph. + --do_at_most (-1) : Only process at most this number of (unprocessed) micrographs. + --grouping_for_ps (-1) : Group this number of frames and write summed power spectrum. -1 == do not write + --ps_size (512) : Output size of power spectrum + --first_frame_sum (1) : First movie frame used in output sum (start at 1) + --last_frame_sum (-1) : Last movie frame used in output sum (0 or negative: use all) + --eer_grouping (40) : EER grouping + --eer_upsampling (1) : EER upsampling (1 = 4K or 2 = 8K) + ====== MOTIONCOR2 options ===== + --use_motioncor2 (false) : Use Shawn Zheng's MOTIONCOR2. + --motioncor2_exe () : Location of MOTIONCOR2 executable (or through RELION_MOTIONCOR2_EXECUTABLE environment variable) + --bin_factor (1) : Binning factor (can be non-integer) + --bfactor (150) : B-factor (in pix^2) that will be used inside MOTIONCOR2 + --gainref () : Location of MRC file with the gain reference to be applied + --gain_rot (0) : Rotate the gain reference this number times 90 degrees clock-wise (in relion_display). This is same as MotionCor2's RotGain. 0, 1, 2 or 3 + --gain_flip (0) : Flip the gain reference. This is same as MotionCor2's FlipGain. 0, 1 (flip Y == upside down) or 2 (flip X == left to right) + --patch_x (1) : Patching in X-direction for MOTIONCOR2 + --patch_y (1) : Patching in Y-direction for MOTIONCOR2 + --group_frames (1) : Average together this many frames before calculating the beam-induced shifts + --defect_file () : Location of a MOTIONCOR2-style detector defect file (x y w h) or a defect map (1 means bad) + --archive () : Location of the directory for archiving movies in 4-byte MRC format + --other_motioncor2_args () : Additional arguments to MOTIONCOR2 + --gpu () : Device ids for each MPI-thread, e.g 0:1:2:3 + ====== Dose-weighting options ===== + --dose_weighting (false) : Use dose-weighting scheme + --angpix (-1) : Pixel size in Angstroms + --voltage (-1) : Voltage (in kV) for dose-weighting + --dose_per_frame (1) : Electron dose (in electrons/A2/frame) for dose-weighting + --preexposure (0) : Pre-exposure (in electrons/A2) for dose-weighting + ====== Own motion correction options ===== + --use_own (false) : Use our own implementation of motion correction + --skip_defect (false) : Skip hot pixel detection + --save_noDW (false) : Save aligned but non dose weighted micrograph + --max_iter (5) : Maximum number of iterations for alignment. Only valid with --use_own + --interpolate_shifts (false) : (EXPERIMENTAL) Interpolate shifts + --ccf_downsample (0) : (EXPERT) Downsampling rate of CC map. default = 0 = automatic based on B factor + --early_binning (false) : Do binning before alignment to reduce memory usage. This might dampen signal near Nyquist. (ON by default) + --no_early_binning (false) : Disable --early_binning + --dose_motionstats_cutoff (4.) : Electron dose (in electrons/A2) at which to distinguish early/late global accumulated motion in output statistics + --version : Print RELION version and exit + +``relion_helix_toolbox`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Show usage ===== + --function_help (false) : Show usage for the selected function (FEB 19, 2017) + ====== List of functions (alphabetically ordered) ===== + --check (false) : Check parameters for 3D helical reconstruction in RELION + --cut_out (false) : Cut out a small part of the helix + --cylinder (false) : Create a cylinder as 3D initial reference + --impose (false) : Impose helical symmetry (in real space) + --interpo (false) : Interpolate 3D curve for 3D helical sub-tomogram extraction + --norm (false) : Normalise 2D/3D helical segments in a STAR file + --pdb_helix (false) : Simulate a helix from a single PDB file of protein molecule + --remove_bad_ctf (false) : Remove micrographs with poor-quality CTF + --remove_bad_tilt (false) : Remove helical segments with large tilt angle deviation (away from 90 degrees) + --remove_bad_psi (false) : Remove helical segments with large psi angle deviation (away from psi prior) + --search (false) : Local search of helical symmetry + --select_3dtomo (false) : Select 3D subtomograms given 2D projections + --simulate_helix (false) : Create a helical 3D reference of spheres + --simulate_segments (false) : Simulate helical segments using a STAR file + --sort_tube_id (false) : Sort segments in _data.star file according to helical tube IDs + --spherical_mask (false) : Apply soft spherical mask to 3D helical reference + --average_au_2d (false) : Average multiple asymmetrical units in 2D along the helical axis? + ====== List of functions which can be called in Relion GUI ===== + --combine_gctf (false) : Combine Autopicker priors (tilt and psi) with Gctf local search results + --central_mask (false) : Crop the central part of a helix + --coords_emn2rln (false) : Convert EMAN2 coordinates of helical segments into RELION STAR format + --coords_xim2rln (false) : Convert XIMDISP coordinates of helical segments into RELION STAR format + --divide (false) : Divide one huge STAR file into many small ones + --extract_emn (false) : Extract EMAN2 coordinates of helical segments from specified straight tubes + --extract_rln (false) : Extract RELION coordinates of helical segments from specified straight tubes + --extract_xim (false) : Extract XIMDISP coordinates of helical segments from specified straight tubes + --impose_fourier (false) : Impose helical symmetry (simulate what is done in 3D reconstruction in Fourier space) + --init_tilt (false) : Set tilt angles to 90 degrees for all helical segments + --merge (false) : Merge small STAR files into a huge one + --set_xmipp_origin (false) : Set Xmipp origin + --debug (false) : (Debug only) + ====== Parameters (alphabetically ordered) ===== + --3d_tomo (false) : Simulate 3D subtomograms using a STAR file? + --ang (91.) : Cut out a small part of the helix within this angle (in degrees) + --angpix (1.) : Pixel size (in Angstroms) + --bimodal (false) : Do bimodal searches of tilt and psi angles in 3D helical reconstruction? + --bin (1) : Binning factor used in manual segment picking + --boxdim (-1) : Box size (in pixels) + --center_pdb (false) : Translate all atoms in the original PDB to the center of mass of this molecule? + --ctf_fom_min (-999) : Minimum figure-of-merit - threshold used in removing micrographs with bad CTF + --cyl_inner_diameter (-1) : Inner diameter of the cylindrical mask (in Angstroms) + --cyl_outer_diameter (-1) : Outer diameter of the cylindrical mask (in Angstroms) + --df_min (-999999.) : Minimum defocus (in Angstroms) + --df_max (999999.) : Maximum defocus (in Angstroms) + --EPA_lowest_res (999) : Lowest EPA resolution (in Angstroms) - threshold used in removing micrographs with bad CTF + --i (file.in) : Input file + --i1 (file01.in) : Input file #1 + --i2 (file02.in) : Input file #2 + --i_root (_rootnameIn.star) : Rootname of input files + --i1_root (_rootnameIn01.star) : Rootname #1 of input files + --i2_root (_rootnameIn02.star) : Rootname #2 of input files + --ignore_helical_symmetry (false) : Ignore helical symmetry in 3D reconstruction? + --nr_asu (1) : Number of helical asymmetrical units + --nr_outfiles (10) : Number of output files + --nr_subunits (-1) : Number of helical subunits + --nr_tubes (-1) : Number of helical tubes + --o (file.out) : Output file + --o_root (_rootnameOut.star) : Rootname of output files + --polar (false) : Construct a 3D reference for helical reconstruction with polarity along Z axis? + --psi_max_dev (15.) : Maximum deviation of psi angles allowed (away from psi prior) + --random_seed (-1) : Random seed (set to system time if negative) + --rise (-1) : Helical rise (in Angstroms) + --rise_inistep (-1) : Initial step of helical rise search (in Angstroms) + --rise_min (-1) : Minimum helical rise (in Angstroms) + --rise_max (-1) : Maximum helical rise (in Angstroms) + --seam_nr_filaments (-1) : Number of filaments in a helix with seam (>= 2) + --search_sym (false) : Perform local searches of helical symmetry in 3D reconstruction? + --segments (false) : Cut helical tubes into segments? + --sigma_offset (5.) : Sigma of translational offsets (in pixels) + --sigma_psi (5.) : Sigma of psi angles (in degrees) + --sigma_tilt (5.) : Sigma of tilt angles (in degrees) + --sphere_percentage (0.9) : Diameter of spherical mask divided by the box size (0.10~0.90 or 0.01~0.99) + --subunit_diameter (-1) : Diameter of helical subunits (in Angstroms) + --sym_Cn (1) : Rotational symmetry Cn + --tilt_max_dev (15.) : Maximum deviation of tilt angles allowed (away from +90 degrees) + --topbottom_ratio (0.5) : Top-bottom width ratio for construction of polarised helical reference + --twist (-1) : Helical twist (in degrees, + for right-handedness) + --twist_inistep (-1) : Initial step of helical twist search (in degrees) + --twist_min (-1) : Minimum helical twist (in degrees, + for right-handedness) + --twist_max (-1) : Maximum helical twist (in degrees, + for right-handedness) + --verb (false) : Detailed screen output? + --white_noise (1.) : Standard deviation of added white Gaussian noise + --width (5.) : Width of cosine soft edge (in pixels) + --xdim (4096) : Dimension X (in pixels) of the micrographs + --ydim (4096) : Dimension Y (in pixels) of the micrographs + --z_percentage (0.3) : Percentage of cropped length (along Z axis, 0.1~0.9) + --version : Print RELION version and exit + +``relion_motion_refine`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input STAR file + --o : Output directory, e.g. MotionFit/job041/ + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --first_frame (1) : First move frame to process + --last_frame (-1) : Last movie frame to process (default is all) + --only_do_unfinished (false) : Skip those steps for which output files already exist. + --verb (1) : Verbosity + ====== Motion fit options (basic) ===== + --fdose (-1) : Electron dose per frame (in e^-/A^2) + --s_vel (0.5) : Velocity sigma [Angst/dose] + --s_div (5000.0) : Divergence sigma [Angst] + --s_acc (2.0) : Acceleration sigma [Angst/dose] + --params_file () : File containing s_vel, s_div and s_acc (overrides command line parameters) + --only_group (-1) : Only align micrographs containing particles from this optics group (negative means off) + --diag (false) : Write out diagnostic data + ====== Motion fit options (advanced) ===== + --cc_pad (1.0) : Cross-correlation Fourier-padding + --dmg_a ( 3.40) : Damage model, parameter a + --dmg_b (-1.06) : b + --dmg_c (-0.54) : c + --max_iters (10000) : Maximum number of iterations + --eps (1e-5) : Terminate optimization after gradient length falls below this value + --no_whiten (false) : Do not whiten the noise spectrum + --unreg_glob (false) : Do not regularize global component of motion + --glob_off (false) : Compute initial per-particle offsets + --glob_off_max (10) : Maximum per-particle offset range [Pixels] + --absolute_params (false) : Do not scale input motion parameters by dose + --debug_opt (false) : Write optimization debugging info + --gi (false) : Initialize with global trajectories instead of loading them from metadata file + --sq_exp_ker (false) : Use a square-exponential kernel instead of an exponential one + --max_ed (-1) : Maximum number of eigendeformations + --out_cut (false) : Do not consider frequencies beyond the 0.143-FSC threshold for alignment + ====== Parameter estimation ===== + --params2 (false) : Estimate 2 parameters instead of motion + --params3 (false) : Estimate 3 parameters instead of motion + --align_frac (0.5) : Fraction of pixels to be used for alignment + --eval_frac (0.5) : Fraction of pixels to be used for evaluation + --min_p (1000) : Minimum number of particles on which to estimate the parameters + --par_group (-1) : Estimate parameters for this optics group only (negative means all) + --s_vel_0 (0.6) : Initial s_vel + --s_div_0 (10000) : Initial s_div + --s_acc_0 (3) : Initial s_acc + --in_step (3000) : Initial step size in s_div + --conv (30) : Abort when simplex diameter falls below this + --par_iters (100) : Max. number of iterations + --mot_range (50) : Limit allowed motion range [Px] + --seed (23) : Random seed for micrograph selection + ====== Combine frames options ===== + --combine_frames (false) : Combine movie frames into polished particles. + --scale (-1) : Re-scale the particles to this size (by default read from particles star file) + --window (-1) : Re-window the particles to this size (in movie-pixels; by default read from particles star file) + --crop (-1) : Crop the scaled particles to this size after CTF pre-multiplication + --ctf_multiply (false) : Premultiply by CTF. + --bfac_minfreq (20) : Min. frequency used in B-factor fit [Angst] + --bfac_maxfreq (-1) : Max. frequency used in B-factor fit [Angst] + --bfactors () : A .star file with external B/k-factors + --diag_bfactor (false) : Write out B/k-factor diagnostic data + --suffix () : Add this suffix to shiny MRCS and STAR files + --recenter (false) : Re-center particle according to rlnOriginX/Y in --reextract_data_star STAR file + --recenter_x (0.) : X-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_y (0.) : Y-coordinate (in pixel inside the reference) to recenter re-extracted data on + --recenter_z (0.) : Z-coordinate (in pixel inside the reference) to recenter re-extracted data on + ====== Computational options ===== + --j (1) : Number of (OMP) threads + --min_MG (0) : First micrograph index + --max_MG (-1) : Last micrograph index (default is to process all) + --sbs (false) : Load movies slice-by-slice to save memory (slower) + ====== Expert options ===== + --corr_mic : List of uncorrected micrographs (e.g. corrected_micrographs.star) + --find_shortest (false) : Load only as many frames as are present in all movies. + --debug (false) : Write debugging data + --mps (-1) : Pixel size of input movies (Angst/pix) + --cps (-1) : Pixel size of particle coordinates in star-file (Angst/pix) + --hot (-1) : Clip hot pixels to this max. value (-1 = off, TIFF only) + --debug_mov (false) : Write debugging data for movie loading + --mov_toReplace () : Replace this string in micrograph names... + --mov_replaceBy () : ..by this one + --eer_upsampling (-1) : EER upsampling (1 = 4K or 2 = 8K) + --eer_grouping (-1) : EER grouping + --version : Print RELION version and exit + +``relion_pipeliner`` +--------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Check job completion options ===== + --check_job_completion (false) : Use this flag to only check whether running jobs have completed + ====== Add scheduled jobs options ===== + --addJobFromStar () : Add a job with the type and options as in this job.star to the pipeline + --addJob () : Add a job of this type to the pipeline + --addJobOptions () : Options for this job (either through --addJobFromStar or --addJob) + --setJobAlias () : Set an alias to this job + ====== Run scheduled jobs options ===== + --RunJobs () : Run these jobs + --schedule () : Name of the scheduler for running the scheduled jobs + --overwrite_jobs (false) : Use this flag to overwrite existing jobs, instead of continuing them + --repeat (1) : Run the scheduled jobs this many times + --min_wait (0) : Wait at least this many minutes between each repeat + --min_wait_before (0) : Wait this many minutes before starting the running the first job + --sec_wait_after (10) : Wait this many seconds after a process finishes (workaround for slow IO) + ====== Expert options ===== + --pipeline (default) : Name of the pipeline + --gentle_clean (-1) : Gentle clean this job + --harsh_clean (-1) : Harsh clean this job + --version : Print RELION version and exit + +``relion_star_datablock_ctfdat`` +--------------------------------------------------------------------------- + +.. code-block:: text + + === Usage: === + /relion_star_datablock_ctfdat + + === Purpose: === + This (bash) script generates the STAR datablock for all images in an xmipp-format CTFDAT file + Note that the sign for XMIPP's defocusU, defocusV and Q0 values is reversed + + === Example: === + /relion_star_datablock_ctfdat all_images.ctfdat + +``relion_import`` +------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input (wildcard) filename + --odir : Output directory (e.g. "Import/job001/" + --ofile : Output file name (e.g. "movies.star" + --do_movies (false) : Import movies + --do_micrographs (false) : Import micrographs + --do_coordinates (false) : Import coordinates + --do_halfmaps (false) : Import unfiltered half maps + --do_particles (false) : Import particle STAR files + --particles_optics_group_name () : Rename optics group for all imported particles (e.g. "opticsGroupLMBjan2019" + --do_other (false) : Import anything else + ====== Specific options for movies or micrographs ===== + --optics_group_name (opticsGroup1) : Name for this optics group + --optics_group_mtf () : Name for this optics group's MTF + --angpix (1.0) : Pixel size (Angstrom) + --kV (300) : Voltage (kV) + --Cs (2.7) : Spherical aberration (mm) + --Q0 (0.1) : Amplitude contrast + --beamtilt_x (0.0) : Beam tilt (X; mrad) + --beamtilt_y (0.0) : Beam tilt (Y; mrad) + --continue (false) : Continue and old run, add more files to the same import directory + --version : Print RELION version and exit + +``relion_scheduler`` +--------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --schedule : Directory name of the schedule + --copy () : Make a copy of the schedule into this directory + ====== Add elements to the schedule ===== + --add () : Specify category of element to add to the schedule (variable, operator, job, edge or fork) + --type () : Specify type of that element to add to the schedule + --i () : Specify input to the element + --i2 () : Specify 2nd input to the element + --bool () : Name of boolean variable (for forks) + --o () : Specify output of the element + --o2 () : Specify 2nd output of the element + --name () : Name of the variable or job to be added + --value () : Value of the variable to be added + --original_value () : Original value of the variable to be added + --mode () : Mode (for jobs): new, overwrite or continue + ====== Set values of variables in the schedule ===== + --reset (false) : Reset all variables to their original values + --abort (false) : Abort a schedule that is running + --set_var () : Name of a variable to set (using also the --value argument) + --set_job_mode () : Name of a job whose mode to set (using also the --value argument) + --set_current_node () : Name of a node to which to set current_node + ====== Run the scheduler within a pipeline ===== + --run (false) : Run the scheduler + --verb (1) : Running verbosity: 0, 1, 2 or 3) + --run_pipeline (default) : Name of the pipeline in which to run this schedule + --version : Print RELION version and exit + + Different ways of using this program: + + ++ Add a variable (of type float, bool or file): + --schedule test --add variable --name iter --value 0 + --schedule test --add variable --name is_finished --value False + --schedule test --add variable --name initial_model --value map.mrc + + ++ Add an operator node (of type float, bool or file): + --schedule test --add operator --type float=plus --i iter --i2 iter_step --o iter + --schedule test --add operator --type float=plus --i iter --i2 1 --o iter + --schedule test --add operator --type touch_file --i initial_model + --schedule test --add operator --type bool=gt --i iter --i2 10 --o is_finished + --schedule test --add operator --type bool=file_exists --i initial_model --o is_finished + + ++ Add a job node: + --schedule test --add job --i my_import --mode continue/new/overwrite + --schedule test --add job --i exit + + ++ Add an edge: + --schedule test --add edge --i inputnodename --o outputnodename + + ++ Add a fork: + --schedule test --add fork --i inputnodename --bool boolvar --o outputnodename --o2 outputnodename_if_false + TODO: add information about setting variables etc too! + + +``relion_autopick_mpi`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Micrograph STAR file OR filenames from which to autopick particles, e.g. "Micrographs/*.mrc" + --pickname (autopick) : Rootname for coordinate STAR files + --odir (AutoPick/) : Output directory for coordinate files (default is to store next to micrographs) + --angpix (1) : Pixel size of the micrographs in Angstroms + --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms, default=automatic) + --shrink_particle_mask (2) : Shrink the particle mask by this many pixels (to detect Einstein-from-noise classes) + --outlier_removal_zscore (8.) : Remove pixels that are this many sigma away from the mean + --write_fom_maps (false) : Write calculated probability-ratio maps to disc (for re-reading in subsequent runs) + --no_fom_limit (false) : Ignore default maximum limit of 30 fom maps being written + --read_fom_maps (false) : Skip probability calculations, re-read precalculated maps from disc + --skip_optimise_scale (false) : Skip the optimisation of the micrograph scale for better prime factors in the FFTs. This runs slower, but at exactly the requested resolution. + --only_do_unfinished (false) : Only autopick those micrographs for which the coordinate file does not yet exist + --gpu (false) : Use GPU acceleration when availiable + ====== References options ===== + --ref () : STAR file with the reference names, or an MRC stack with all references, or "gauss" for blob-picking + --angpix_ref (-1) : Pixel size of the references in Angstroms (default is same as micrographs) + --invert (false) : Density in micrograph is inverted w.r.t. density in template + --ang (10) : Angular sampling (in degrees); use 360 for no rotations + --lowpass (-1) : Lowpass filter in Angstroms for the references (prevent Einstein-from-noise!) + --highpass (-1) : Highpass filter in Angstroms for the micrographs + --ctf (false) : Perform CTF correction on the references? + --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? + --gauss_max (0.1) : Value of the peak in the Gaussian blob reference + --healpix_order (1) : Healpix order for projecting a 3D reference (hp0=60deg; hp1=30deg; hp2=15deg) + --sym (C1) : Symmetry point group for a 3D reference + ====== Laplacian-of-Gaussian options ===== + --LoG (false) : Use Laplacian-of-Gaussian filter-based picking, instead of template matching + --LoG_diam_min (-1) : Smallest particle diameter (in Angstroms) for blob-detection by Laplacian-of-Gaussian filter + --LoG_diam_max (-1) : Largest particle diameter (in Angstroms) for blob-detection by Laplacian-of-Gaussian filter + --LoG_neighbour (100) : Avoid neighbouring particles within (the detected diameter + the minimum diameter) times this percent + --Log_invert (false) : Use this option if the particles are white instead of black + --LoG_adjust_threshold (0.) : Use this option to adjust the picking threshold: positive for less particles, negative for more + --LoG_upper_threshold (99999) : Use this option to set the upper limit of the picking threshold + --LoG_use_ctf (false) : Use CTF until the first peak in Laplacian-of-Gaussian picker + ====== Helix options ===== + --helix (false) : Are the references 2D helical segments? If so, in-plane rotation angles (psi) are estimated for the references. + --helical_tube_kappa_max (0.25) : Factor of maximum curvature relative to that of a circle + --helical_tube_outer_diameter (-1) : Tube diameter in Angstroms + --helical_tube_length_min (-1) : Minimum tube length in Angstroms + --amyloid (false) : Activate specific algorithm for amyloid picking? + ----max_diam_local_avg (-1) : Maximum diameter to calculate local average density in Angstroms + ====== Peak-search options ===== + --threshold (0.25) : Fraction of expected probability ratio in order to consider peaks? + --min_distance (-1) : Minimum distance (in A) between any two particles (default is half the box size) + --max_stddev_noise (-1) : Maximum standard deviation in the noise area to use for picking peaks (default is no maximum) + --min_avg_noise (-999.) : Minimum average in the noise area to use for picking peaks (default is no minimum) + --skip_side (0) : Keep this many extra pixels (apart from particle_size/2) away from the edge of the micrograph + ====== Expert options ===== + --verb (1) : Verbosity + --pad (2) : Padding factor for Fourier transforms + --random_seed (1) : Number for the random seed generator + --shrink (1.0) : Reduce micrograph to this fraction size, during correlation calc (saves memory and time) + --Log_max_search (5.) : Maximum diameter in LoG-picking multi-scale approach is this many times the min/max diameter + --extra_pad (0) : Number of pixels for additional padding of the original micrograph + --version : Print RELION version and exit + +``relion_convert_to_tiff`` +--------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General Options ===== + --i : Input movie to be compressed (an MRC/MRCS file or a list of movies as .star or .lst) + --o (./) : Directory for output TIFF files + --only_do_unfinished (false) : Only process non-converted movies. + --j (1) : Number of threads (useful only for --estimate_gain) + --gain () : Estimated gain map and its reliablity map (read) + --thresh (50) : Number of success needed to consider a pixel reliable + --estimate_gain (false) : Estimate gain + ====== EER rendering options ===== + --eer_grouping (40) : EER grouping + --eer_upsampling (1) : EER upsampling (1 = 4K or 2 = 8K) + --short (false) : use unsigned short instead of signed byte for EER rendering + ====== TIFF writing options ===== + --compression (auto) : compression type (none, auto, deflate (= zip), lzw) + --deflate_level (6) : deflate level. 1 (fast) to 9 (slowest but best compression) + --ignore_error (false) : Don't die on un-expected defect pixels (can be dangerous) + --line_by_line (false) : Use one strip per row + --version : Print RELION version and exit + +``relion_postprocess`` +----------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input name of half1, e.g. run_half1_class001_unfil.mrc + --i2 () : Input name of half2, (default replaces half1 from --i with half2) + --o (postprocess) : Output rootname + --angpix (-1) : Pixel size in Angstroms + --half_maps (false) : Write post-processed half maps for validation + --mtf_angpix (-1.) : Pixel size in the original micrographs/movies (in Angstroms) + --molweight (-1) : Molecular weight (in kDa) of ordered protein mass + ====== Masking options ===== + --auto_mask (false) : Perform automated masking, based on a density threshold + --inimask_threshold (0.02) : Density at which to threshold the map for the initial seed mask + --extend_inimask (3.) : Number of pixels to extend the initial seed mask + --width_mask_edge (6.) : Width for the raised cosine soft mask edge (in pixels) + --mask () : Filename of a user-provided mask (1=protein, 0=solvent, all values in range [0,1]) + --force_mask (false) : Use the mask even when the masked resolution is worse than the unmasked resolution + ====== Sharpening options ===== + --mtf () : User-provided STAR-file with the MTF-curve of the detector + --auto_bfac (false) : Perform automated B-factor determination (Rosenthal and Henderson, 2003) + --autob_lowres (10.) : Lowest resolution (in A) to include in fitting of the B-factor + --autob_highres (0.) : Highest resolution (in A) to include in fitting of the B-factor + --adhoc_bfac (0.) : User-provided B-factor (in A^2) for map sharpening, e.g. -400 + ====== Filtering options ===== + --skip_fsc_weighting (false) : Do not use FSC-weighting (Rosenthal and Henderson, 2003) in the sharpening process + --low_pass (0) : Resolution (in Angstroms) at which to low-pass filter the final map (0: disable, negative: resolution at FSC=0.143) + ====== Local-resolution options ===== + --locres (false) : Perform local resolution estimation + --locres_sampling (25.) : Sampling rate (in Angstroms) with which to sample the local-resolution map + --locres_maskrad (-1) : Radius (in A) of spherical mask for local-resolution map (default = 0.5*sampling) + --locres_edgwidth (-1) : Width of soft edge (in A) on masks for local-resolution map (default = sampling) + --locres_randomize_at (25.) : Randomize phases from this resolution (in A) + --locres_minres (50.) : Lowest local resolution allowed (in A) + ====== Expert options ===== + --ampl_corr (false) : Perform amplitude correlation and DPR, also re-normalize amplitudes for non-uniform angular distributions + --randomize_at_fsc (0.8) : Randomize phases from the resolution where FSC drops below this value + --randomize_at_A (-1) : Randomize phases from this resolution (in A) onwards (if positive) + --filter_edge_width (2) : Width of the raised cosine on the low-pass filter edge (in resolution shells) + --verb (1) : Verbosity + --random_seed (0) : Seed for random number generator (negative value for truly random) + --version : Print RELION version and exit + +``relion_tiltpair_plot`` +------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --u : Input STAR file with untilted particles + --t : Input STAR file with tilted particles + --o (tiltpair.eps) : Output EPS file + --sym (C1) : Symmetry point group + --exp_tilt (0.) : Choose symmetry operator that gives tilt angle closest to this value + --exp_beta (0.) : Choose symmetry operator that gives beta angle closest to this value + --dist_from_alpha (0.) : Direction (alpha angle) of tilt axis from which to calculate distance + --dist_from_tilt (0.) : Tilt angle from which to calculate distance + --max_tilt (90.) : Maximum tilt angle to plot in the EPS file + --spot_radius (3) : Radius in pixels of the spots in the tiltpair plot + --version : Print RELION version and exit + +``relion_particle_reposition`` +------------------------------------------------------------------------- + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== Options ===== + --i : Input STAR file with rlnMicrographName's + --opt : Optimiser STAR file with the 2D classes or 3D maps to be repositioned + --o () : Output rootname, to be added to input micrograph names + --odir () : Output directory (default is same as input micrographs directory + --data () : Data STAR file with selected particles (default is to use all particles) + --background (0.1) : The fraction of micrograph background noise in the output micrograph + --invert (false) : Invert the contrast in the references? + --ctf (false) : Apply CTF for each particle to the references? + --norm_radius (-1) : Radius of the circle used for background normalisation (in pixels) + --subtract (false) : Subtract repositioned micrographs from the input ones? + --version : Print RELION version and exit + +``relion_particle_FCC`` +------------------------------------------------------------------ + +.. code-block:: text + + +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ + ====== General options ===== + --i : Input particle *.star file + --f : Input STAR file with the FSC of the reference (usually from PostProcess) + --o : Output path + --m1 () : Reference map, half 1 + --m2 () : Reference map, half 2 + --angpix_ref (-1) : Pixel size of the reference map + --mask () : Reference mask + --pad (2) : Padding factor + --min_freq (0) : Min. image frequency [px] + --opposite_half (false) : Correlate with opposite half-set + --predict_CTF (false) : Modulate prediction by CTF + --min_MG (0) : First micrograph index + --max_MG (-1) : Last micrograph index (default is to process all) + --j (1) : Number of threads + --version : Print RELION version and exit + diff --git a/source/Reference/index.rst b/source/Reference/index.rst index 7887a99..cebcee9 100644 --- a/source/Reference/index.rst +++ b/source/Reference/index.rst @@ -12,4 +12,5 @@ Reference pages Using-RELION Conventions DeveloperGuide + Cli Bibliography