e2align3d

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
	
	e2align3d:
	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