usage: prog --path <path to previous spt or subtlt refinement> [options]
	This program will run subtilt refinement based on previous subtomogram or subtilt refinement.

Option Type Description
--version None show program's version number and exit
--path str Path to the previous spt/subtlt refinement (required)
--iter int Start from iteration X of previous refinement
--niters int Run this many iterations. Default is 4.
--keep float propotion of tilts to keep. default is 0.8
--maxalt float max altitude to insert to volume
--mask str Refinement and reprojection masking. Default uses mask from source
--maskalign str Mask to apply during alignment, but not the final model. Default is to use the same mask.
--nogs None Skip gold standard. This is not a great idea...
--threads int Number of CPU threads to use. Default is 12.
--parallel str Thread/mpi parallelism to use. Default is thread:12
--buildsetonly None will only prepare particle set for the refinement but skip the actual refinement process.
--resume None continue from previous run
--reproject None Reproject 3D particles into 2D particles.
--reprj_offset str Offset translation before reprojection
--reprj_clip int clip after reprojection
--tophat str 'local', 'localwiener' or 'global'. Instead of imposing a uniform Wiener filter, use a tophat filter ('global' similar to Relion). local is a local tophat filter, localwiener is a local Wiener filter
--refineastep float Mean angular variation for refine alignment
--refinentry int number of starting points for refine alignment
--maxshift int maximum shift allowed
--padby float pad by factor. default is 1.5
--debug None Turn on debug mode. This will only process a small subset of the data (threads * 8 particles)
--localnorm None local normalization. do not use yet....
--sym str symmetry. will use symmetry from spt refinement by default
--ppid int ppid...
--transonly None only refine translation
--maxres float max resolution for fsc
--minres float min resolution for fsc