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 .