usage: prog [options] [classes file]
	This program will go through a standard classes file (containing EMAN2-generated class-averages), and extract the
particles associated with one or more class-averages. Some similar tasks can be performed graphically with e2evalparticles.py.
This program is used by e2refinemulti to extract particles associated with each of the output volumes for subsequent
single-model refinement.

There are 3 mutually exclusive modes in this program:
	--refinemulti - Extracts the particles associated with each of the output 3-D maps generated by an e2refinemulti run
	--classlist - Extracts references to all of the particles in a user specified list of class numbers (the list of integers is in a text file)
	--orientedparticles - Extracts rotated/translated particles associated with each class-average into a separate stack (also requires --orientcls)
Extract all of the 2-D aligned even and odd particles associated with a specific class-average:
e2classextract.py --orientcls refine_03/cls_result_04 --orientedparticles sets/all_ctf_flip_fullres --evenoddmerge --orientclassn 248

Option Type Description
--version None show program's version number and exit
--refinemulti None Extracts particles based on the model_id header value in each class-average, normally produced by e2refinemulti
--classlist str Filename of a text file containing a (comma or whitespace separated) list of class average numbers to operate on.
--orientedparticles str Filename of the set (.lst file) with the particles used for the --orientcls file
--orientcls str Filename of a cls_result_xx or classmx_xx file.
--orientclassn str Specify a comma separated list of class numbers to extract in oriented particles mode.
--input_set str Normally the set used to create the class-averages is used as input. Use this with another version of the same set of particles, for example '__ctf_flip_proc' instead of '__ctf_flip'
--setname str Name of the stack to build
--evenoddmerge None with --orientedparticles, if cls_result_xx is specified, will include both _even and _odd particles in the output.
--excludebad None Excludes the particles from the generated set(s). They are included by default.
--noderef None If particle file was .lst, normally the output .lst will reference the original image file. With this option, the output will reference the .lst file instead, creating a lst pointing to another lst.
--sort None If set, output .lst file will be sorted. The default is to leave the output grouped by class-average. If (and only if) sorted, duplicate entries will be removed.
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness

For more information go to emanwiki/EMAN2/Programs/e2classextract.