usage: prog [options] <raw particle file> <class mx> <projections>

This program can use either a 3-D binary mask, or a pair of liganded/unliganded volumes to classify particle data into 2
(or 4) groups. e2refine.py must be run on the data first. The method using a pair of volumes is much more accurate in
separating particles.

This is part of a multi-step process for separating ligand bound from ligand free particles, but relies on sufficient
ligand/no-ligand contrast in individual images:
 1) refine the entire data set with e2refine.py, such that most classes have at least 10-20 particles in them
 2) construct a volume the same size as your reconstruction containing a binary mask, with 1 in the region where the ligand would be
2a) -or- prepare 2 volume files representing the particle with or without associated ligand
 3) run this program

<raw particle file> should be the same file used in the refinement
<class mx> is one of the classification matrix files from the refinement
<projections> contains the projections used for class mx

Typical usage:
e2classifyligand.py sets/myset_even.lst refine_01/classmx_04_even.hdf refine_01/projections_04_even.hdf --ref1 ref3d1.hdf --ref2 ref3d2.hdf --cmp=ccc --plotout=cmp.txt --pairmask --splitparticles -v 1

Option Type Description
--version None show program's version number and exit
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--ref1 str Rather than using a mask, ref1/ref2 permit using a pair of volumes for classification.
--ref2 str Rather than using a mask, ref1/ref2 permit using a pair of volumes for classification.
--pairmask None Will use the ref1/ref2 pair to generate a mask which is applied after subtracting ref1 from the particle
--alistacks float If sum of cmp results is less than the spefified value, will save the aligned particle to a per-class stack
--cmp str The name of a 'cmp' to be used when pairmask is not specified
--process str A processor to apply to the particle data before classifying
--plotout str Name of a text file for the classification plot.
--badgroup None Split the data into 4 groups rather than 2. The extra two groups contain particles more likely to be bad.
--badqualsig float When identifying 'bad' particles, particles with similarities >mean+sigma*badqualsig will be considered bad. Default 0.5
--badsepsig float When identifying 'bad' particles, if s1/s2 are the similarities to reference 1/2, then those where |s1-s2| < sigma*badsepsig will be excluded. Default 0.25
--postfix str This string will be appended to each set name to help differentiate the results from multiple runs
--splitparticles None Specify this to write new files containing the classified particles
--tstcls int Will generate tst.hdf containing test images for a specified class-number
--debug None Enable debugging mode with verbose output and image display. Not suitable for real runs.
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2classifyligand.