Running e2refinetorelion3d.py
usage:  prog [options] <set name> <reference map name>

This program will extract the necessary parameters from an EMAN2 refinement and


       [-] [-] [-] [- RANDOMIZEMODEL] [-] [- SYMMGROUP] [- SYMMNUMBER] [-] [-]
       [- MAXMEMORY] [- AMPLITUDECONTRAST] [-] [-] [-] [- PAD] [- LIMIT_TILT]
       [- VERBOSE] [-] [- PPID]
       [positionalargs ...]

Option Type Description
--version None show program's version number and exit
--randomizemodel None Optionally randomize the phases of the initial model to this resolution (in Angstroms)
--greyscale None Is the reference map in greyscale?
--symmgroup None Symmetry group
--symmnumber int Symmetry number
--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?
--lowpass float Initial low-pass filter for the reference map (Ang)
--particle_mask_diameter float Diameter of the soft spherical image mask in angstroms
--solventmask str Location of the mask to be used
--healpix str Angular Sampling Interval (Degrees)
--auto_healpix str Local angular search value
--offsetrange float Offset search range (pix)
--offsetstep float Offset search step (pix)
--threads int # of threads
--maxmemory float Maximum memory (in GB) available for each thread
--amplitudecontrast float Amplitude Contrast value for the micrographs
--intensitycorrection None (T/F)Perform intensity-scale corrections on image groups?
--print_symmetry None Print all symmetry transformation matrices, and exit
--nearest_neighbor None Perform nearest-neighbor instead of linear Fourier-space interpolation
--pad int Padding factor
--limit_tilt int Limited tilt angle: positive for keeping side views, negative for keeping top views
--verbose int Set the level of verbosity for the code
--onlyflipphase None (T/F)Only flip phases?
--ppid int Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2refinetorelion3d.