usage: prog fixed_model moving_model output_model [options] 

	NOTICE - the development of the much faster tree aligner really makes this program
	obsolete. While this program still works, we generally suggest using e2proc3d.py:
	e2proc3d.py <moving_model> <output> --alignref <fixed_model> --align rotate_translate_3d_tree
	This program is designed to rotationally and translationally align two 3D models 
	Usually the two models are shrunk down to speed things up, then a global exhaustive 
	search is down by the refine.3d.sphere and then this rough alignment is refined using
	refine.3d using the full size maps. The refiner is much quicker than the global aligner
	as it uses a simplex algorithm to bring the alignment downhill, but if your initial global
	alignment is too rough then the refiner might get stuck in a local minima.

Option Type Description
--version None show program's version number and exit
--shrink int Fractional amount to shrink the maps by, default=1
--preprocess str preprocess maps before alignment
--maskrad int Mask the recon using a spherical Gaussian mask (-1 = None), default=-1.0
--maskfoff float Fall offf of the Gaussian mask, default=0.1
--nsolns int number of peaks in the global search to refine, default=1.0
--famps float fraction of Fourier amps to exclude from recons. 0 means that this option is not used, default=0.0
--prec float Precision to determine what solutions are the 'same' used only statistics output, default=0.01
--cuda None Use CUDA for the alignment step.
--delta float step size for the orientation generator, default=30.0
--dphi float step size for the inplane angle phi, default=30.0
--phi0 float lower bound for the inplane angle phi, default=0.0
--phi1 float Upper bound for the inplane angle phi, default=359.0
--search int maximum extent of the translational search, default=10
--sym str model symmetry (using sym, if present, speeds thing up a lot), default='c1'
--cmp str comparitor and params to use for the 3D refiner, default='ccc'
--dotrans int Do translational search, default=1
--ralign str aligner to use for refine alignment, default='refine_3d:spin_coeff=1'
--rcmp str comparitor and params to use for the 3D refiner, default='ccc'
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int Level of verboseness, default=0