Running e2refinetorelion2d.py
usage:  prog [options] <set name>

This program will extract the necessary parameters from an EMAN2 refinement and determine class averages using Relion 2D ML


       [-] [-] [-] [- NUMCLASSES] [-] [-] [-] [- NUMITER] [- REGPARAM]
       [- CS] [- APIX] [- DEFOCUS] [- AMPCONT] [-] [- PPID]
       [positionalargs ...]

Option Type Description
--version None show program's version number and exit
--numclasses int # of classes
--ctfcorrect None (T/F)Do CTF Correction?
--dataphaseflipped None (T/F)Has the data been phase flipped already?
--ignoretofirstpeak None (T/F)Ignore CTF's until the first peak?
--numiter int # of iterations to refine
--regparam float Regularization Parameter T (weights experimental data vs. prior
--particle_mask_diameter float Diameter of the soft circular image mask (in Angstroms)
--maskzeroes None (T/F) For individual particles, the area outside a circle with the radius of the particle will be set to zeros prior to taking the Fourier transform
--solventmask str Location of the mask to be used
--inplaneang float In-plane angular sampling
--offsetrange float Offset search range (pix)
--offsetstep float Offset search step (pix)
--threads int # of threads
--verbosity int Set the level of verbosity for the code
--voltage int (Expert Option) Voltage of the Microscope (kV)
--cs float (Expert Option) Spherical Aberration
--apix float (Expert Option) Angstrom per pixel
--defocus float (Expert Option) Defocus in A
--ampcont float (Expert Option) Amplitude Constrast. 10%% = .1
--echo None Echo Relion Command to terminal only
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2refinetorelion2d.