classesbymra2

This program classifies a set of particles based on multiple sets of references and splits the results between 2 directories.

classesbymra2 <particles> <refrences> <number of sets> [frac=<num>/<denom>] [verbose[=<n>]] [mask=<rad>] [imask=<rad>] [precen] [sigfilt] [ctfc] [shrink=<n>] [refine] [slow] [phase] [wtphase] [fscmp] [wtfscmp] [usefilt]

Parameters:


<particles>Raw particle filespec
<refrences>Reference image filespec
<number of sets>Number of different reference sets
[frac=<num>/<denom>]Operate only on a fraction of the raw images
[verbose[=<n>]]More verbose output
[mask=<rad>]Mask the classified particles, also reduces noise for better classification
[imask=<rad>]Inside mask, classified particles are masked for classification, but not in the cls files.
[precen]Particles are assumed to be accurately precentered
[sigfilt]Apply a real space filter so only high amplitude data is used for classification
[ctfc]Projections are CTF corrected
[shrink=<n>]Shrink the particles before classification by speed
[refine]Refines 2D alignment done with fast algorithm. Slower, but not 'slow'.
[slow]Uses a very slow, exhaustive search algorithm for alignment
[phase]Experimental. Uses pcmp(), a weighted mean phase-error to compare images for classification
[wtphase]Experimental. Uses pcmp with a SNR weight.
[fscmp]Experimental. Uses fscmp(), a weighted mean phase-error to compare images for classification
[wtfscmp]Experimental. Uses fscmp with a SNR weight.
[usefilt]Experimental. Use the 'filt' version of the input file for classification.

Usage:

classesbymra2 start.hed proj.hed 2 mask=28 ctfc

Description

This classifies a set of raw particles based on multiple sets of reference projections. The output is a set of cls*.img files, one file for each reference image. If the projections were generated from a CTF corrected model, specify the 'ctfc' option so the projections will be 'decorrected' before classification.

This is basically a modified version of classesbymra. In this case, a set of numbered directories must exist in the current directory, ie - '1', '2', '3', etc. The file must exist in each subdirectory. specifies how many subdirectories exist.


EMAN Manual page, generated Wed Feb 18 10:51:32 2009