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commented
6 months ago Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2016-03-07T21:19:51Z
Reference for program: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Calculate_2D_class_averages
Installed RELION inside docker Needed to use FLTK v1.3.0 (CentOS only had v1.1.10) Native FFTW 3.2.1 (RELION came with 3.2.2)
Annoyed that I had to open the GUI to figure out what program to run. Appears to use relion_refine as its main program.
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--dont_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 master process read all particles into memory. Be careful you have enough RAM for large data sets!
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution 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?)
Author Name: Neil Voss (@vosslab) Original Redmine Issue: 3971, https://emg.nysbc.org/redmine/issues/3971 Original Date: 2016-02-19 Original Assignee: Carl Negro
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