command_line_dictionary_simple2
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SIMPLE 2.0 command line dictionary acf amsklp bin box boxpd center clsdoc cure cwd debug deterministic discrete doalign dopca doprint e1 e2 e3 edge eo even fbody filter frac fromp froms gw hp kmeans local lp matched maxits minp moldiam msk mskfile mul mw navgs ncls ndiscrete ndocs newbox autocorrelation function automask low-pass limit (in Å) binarize (yes|no) image size in pixels (image assumed to be box*box array) padded box size (default is 2*box) center(yes|no) Spider format clustering document cure or not (yes|no), for curing NaN:s and normalize current working directory debug mode (yes|no) deterministic search (yes|no) discrete option (yes|no) do alignment (yes|no) do PCA (yes|no) do print (yes|no) first Euler angle second Euler angle third Euler angle edge size for softening molecular envelope (in pixels) even-odd test (yes|no) even (yes|no) file body (<body>.ext) filter (yes|no) fraction [0,1] from particle index from state index Gaussian half width (in pixels) high-pass limit (in Å) do kmeans (yes|no) local refinement (yes|no) low-pass limit (in Å) use matched Wiener filter (yes|no) maximum number of iterations minimum number of particle images (in a cluster) molecular diameter (in Å) circular or spherical mask radius (in pixels) external mask file (*.spi) multiplication (scaling) factor (for shifts) molecular weight (in kD) number of averages number of clusters number of discrete (orientations) number of documents new box size noise noris norm npart npeaks nptcls nran nspace nstates nthr nvars nvox oritab outfile outstk outvol part pgrp phrand phranlp ppca ring1 ring2 rnd roalgn shalgn smpd snr space startit state stk stk2 stk3 tau time_per_image top tos tres trs trsstep utst var vol1 wfun winsz noise (yes|no) number of orientations normalize (yes|no) number of partitions number of peaks (=number of nonzero orientation weights) number of particle images number of images in random sample number of projection directions in search space number of discrete state groups number of openMP threads number of eigenvectors or hidden variables number of voxels SIMPLE orientations file (*.txt) SIMPLE output file (*.txt) output Spider image stack (*.spi suffix required) output Spider volume (*.spi suffix required) partition number point-group symmetry (c1, c2, c3, …, or d1, d2, d3, …) phase randomize (yes|no) phase randomization low-pass limit (in Å) probabilistic pca (yes|no) inner ring in polar image representation outer ring in polar image representation random (yes|no) rotational alignment (yes|no) shift alignment (yes|no) sampling distance (in Å) signal-to-noise ratio space (real|fourier) starting iteration (if different than 1) discrete state group spider image stack name (*.spi suffix required) second spider image stack name (*.spi suffix required) third spider image stack name (*.spi suffix required) temperature parameter per particle time indicator to particle index to state index threshold origin shift search range parameter [-trs,trs] translation step size unit test number variance spider volume 1 name (*.spi suffix required) weighting function or interpolation kernel window size for interpolation zero zero (yes|no)
