e2spt_align

usage: Usage: e2spt_align.py [options] <subvolume_stack> <reference>
This program is part of the 'new' hierarchy of e2spt_ programs. It performs one iteration of a classical subtomogram refinement, ie -  aligning particles with missing wedge to a reference in 3-D

The reference may be <volume> or <volume>,<n>

If --goldstandard is specified, even and odd variants of the alignment reference must be provided, and even and odd particles will be aligned separately

Option	Type	Description
--version	None	show program's version number and exit
--threads	int	Number of alignment threads to run in parallel on a single computer. This is the only parallelism supported by e2spt_align at present.
--iter	int	Iteration number within path. Default = start a new iteration
--goldstandard	float	If specified, will phase randomize the even and odd references past the specified resolution (in A, not 1/A)
--goldcontinue	None	Will use even/odd refs corresponding to specified reference to continue refining without phase randomizing again
--mask	str	Mask file aligned to the input reference. Alignment occurs under this mask.
--path	str	Path to a folder where results should be stored, following standard naming conventions (default = spt_XX)
--sym	str	Symmetry of the input. Must be aligned in standard orientation to work properly.
--maxres	float	Maximum resolution (the smaller number) to consider in alignment (in A, not 1/A)
--minres	float	Minimum resolution (the larger number) to consider in alignment (in A, not 1/A)
--nsoln	int	number of solutions to keep at low resolution for the aligner
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--parallel	str	Thread/mpi parallelism to use
--transonly	None	translational alignment only, for prealigned particles
--refine	None	local refinement from xform.align3d in header.
--flcf	None	use slower aligner (experimental)
--refinentry	int	number of tests for refine mode. default is 8
--randphi	None	randomize phi during refine alignment
--breaksym	None	symmetry breaking.
--breaksymsym	str	the symmetry to use for breaksym. setting sym to c6 and this to c2 results in a c3 structure. default is the same as sym
--rand180	None	randomly add a 180 degree rotation during refine alignment
--test180	None	Test for improved alignment with 180 degree rotations even during refine alignment
--skipali	None	skip alignment. the program will do nothing. mostly for testing...
--maxang	float	Maximum angular difference for the refine mode. default is 30
--maxshift	float	Maximum shift for the refine mode. default is 16
--scipytest	None	test scipy optimizer.
--debug	None	.