usage: prog [options]
	This program will take a set of reference-free class-averages (or other projections) and generate a set of possible
	3-D initial models. It does this by heavily downsampling the data, then running a number of very fast, full iterative
	refinements, each seeded with a random starting model. The results are sorted in order of apparent agreement with the
	data, such that at the end, the first numbered model should be the best result. Ideally the top few answers will all
	qualtitatively agree on the overall structure. If they do not, the results should be thoroughly assessed manually to
	insure a sensible result. By default this routine will generate 10 initial models, but this may be fewer or more than
	is strictly necessary depending on a number of factors. If the data is highly structurally heterogeneous, particularly
	if combined with a strongly preferred orientation, a correct solution using this technique may not be possible, but
	for most situations it will work well. For other situations, single particle tomography presents a good alternative
	for generating initial models.

Option Type Description
--version None show program's version number and exit
--input str This file should contain good class-averages to use in constructing the initial model
--iter int The total number of refinement iterations to perform, typically 5-10
--tries int The number of different initial models to generate in search of a good one
--shrink int Optionally shrink the input particles by an integer factor prior to reconstruction. Default=0, no shrinking
--sym None Specify symmetry - choices are: c<n>, d<n>, h<n>, tet, oct, icos
--automaskexpand int Number of voxels of post-threshold expansion in the mask, for use when peripheral features are truncated. (default=shrunk boxsize/20)
--randorient None Instead of seeding with a random volume, seeds by randomizing input orientations
--maskproc str Default=none. If specified, this mask will be performed after the built-in automask, eg - mask.soft to remove the core of a virus
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--orientgen str The type of orientation generator. Default is eman:delta=9.0:inc_mirror=0:perturb=1. See e2help.py orientgens
--parallel, -P str Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2initialmodel.