usage: Perform a mult-model refinement without alignment. Default is to generate classes randomly (--ncls) then iterate to converge. Alternatively, multiple --ref options may be provided.

Option Type Description
--version None show program's version number and exit
--path str Output path, default=sptcls_XX
--ncls int Number of classes to generate. Specify this or multiple --ref options. Default 2
--ref None 3D reference for iterative alignment/averaging. <name> or <name>,#. For multiple references use this option multiple times. Refs autogenerated if this is not specified.
--niter int number of iterations
--maxres float max resolution in A
--parm str particle_parms_xx.json file from spt_refine, this provides both the input particles and alignment parameters
--strucfac str Structure factor file
--parallel str parallel
--mask str mask file
--sym str
--applysym str
--symcopy None Copy each particle for each asymetrical unit. need a maskclass to focus on one unit. do not work with applysym
--randsym None randomize symmetry unit assignment at the begining. seems to be helpful for high symmetry without obvious asymetrical features..