usage: prog <particle stack> --ref <reference> [options]
	Iterative subtomogram refinement.  

Option Type Description
--version None show program's version number and exit
--ref None 3D reference for iterative alignment/averaging. <name> or <name>,#. For multiple references use this option multiple times. The first reference will be used for alignment.
--mask str Mask file to be applied to initial model
--maskalign str Mask file applied to 3D alignment reference in each iteration. Not applied to the average, which will follow normal masking routine.
--maskclass str Mask file applied to 3D classification references in each iteration. Not applied to the average.
--niter int Number of iterations
--sym str symmetry
--setsf str structure factor
--maxtilt float Explicitly zeroes data beyond specified tilt angle. Assumes tilt axis exactly on Y and zero tilt in X-Y plane. Default 90 (no limit).
--restarget float Filters each map at the end of each iteration to this resolution (in A) since FSC isn't available
--path str Specify name of refinement folder. Default is spt_XX.
--maxang float maximum anglular difference in refine mode.
--maxshift float maximum shift in pixel.
--ppid int Set the PID of the parent process, used for cross platform PPID
--threads int threads
--parallel str Thread/mpi parallelism to use
--transonly None translational alignment only
--refine None local refinement from xform in header.
--randphi None randomize phi for refine search
--rand180 None include 180 degree rotation for refine search
--scipy None test scipy refinement