e2spt_refinemulti_new

usage: 
	Multi-reference classification for the new (2021) SPT refinement protocol. Since gold-standard validation is not used here, setting a --maxres is necessary. 
	e2spt_refinemulti_new.py ref1.hdf ref2.hdf --ptcls sets/ptcls.lst --niter 5 --maxres 20
	
	Alternatively, specify a number of classes instead of providing multiple references
	e2spt_refinemulti_new.py ref.hdf --ptcls sets/ptcls.lst --niter 5 --maxres 20 --nref 3
	
	If an existing single model refinement exist, provide the aliptcls3d_xx.lst file as particles and use --loadali3d. reference maps are not necessary in this case.
	e2spt_refinemulti_new.py --ptcls spt_xx/aliptcls3d_yy.lst --niter 5 --maxres 20 --nref 3 --loadali3d

Option	Type	Description
--version	None	show program's version number and exit
--ptcls	str	Particle input. required
--path	str	Path for the refinement
--nref	int	Number of classes. Without --loadali3d, it duplicate the first ref N times with phase randomization at 2 x maxres. With --loadali3d, the particles are classified to N random classes at the begining.
--maskalign	str	Mask file applied to 3D alignment reference in each iteration. Not applied to the average, which will follow normal masking routine.
--maskref	str	Mask applied to the references prior to classification
--maxres	float	Maximum resolution (the smaller number) to consider in alignment (in A, not 1/A). Default is 20A
--minres	float	Minimum resolution (the larger number) to consider in alignment (in A, not 1/A)
--niter	int	number of iterations. default is 5.
--loadali3d	None	load previous 3d alignment from --ptcls input.
--skipali	None	Skip alignment entirely when --loadali3d is provided. Otherwise a local orientation search will still be performed.
--parallel	str	parallel options
--sym	str	symmetry to apply to the average structure
--breaksym	str	Break specified symmetry. Only used when --loadali3d is on.
--setsf	str	set structure factor from text file
--maxshift	int	maximum shift for local alignment. default box size/6
--maxang	int	maximum angle difference for local alignment.