usage: e2ptclvsmap.py [options]

This program is used to visually, and somewhat quantitatively, assess how well a set of particles actually agree with a given 3-D map.

Provide a 3-D map, and a set of particles. The program will classify and align all of the particles, matching each with it's best-matching 
projection, very much like the first step in 3-D refinement. Once classified, each particle is compared to its associated projection and
the set of per-projection particles is sorted in order of similarity. An output file is then created containing each projection
followed by a sorted list of associated particles for each.

The reason this script does not just extract similar information from a refine_xx folder is to avoid the map perturbations which occur in
gold-standard refinement.

Option Type Description
--version None show program's version number and exit
--input str The name of the image file containing the particle data
--model str The map to use as a starting point for refinement
--filterout None Filters output particles to match projections
--angstep float Angular separation of projections. Default 9.0 degrees.
--sym None Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.
--simalign str Default=auto. The name of an 'aligner' to use prior to comparing the images
--simaligncmp str Default=auto. Name of the aligner along with its construction arguments
--simralign str Default=auto. The name and parameters of the second stage aligner which refines the results of the first alignment
--simraligncmp str Default=auto. The name and parameters of the comparitor used by the second stage aligner.
--simcmp str Default=auto. The name of a 'cmp' to be used in comparing the aligned images
--parallel, -P str Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--threads int Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful
--path str The name of a directory where results are placed. Default = create new ptclmap_xx
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness