usage: prog [options]

	This program performs the post-processing steps for e2refine_easy. This gives an easy way to re-run the post-processing if necessary.

Option Type Description
--version None show program's version number and exit
--even str The filename of the map from the even 1/2 of the data
--odd str The filename of the map from the odd 1/2 of the data
--output str Filename for the final averaged/filtered result.
--compressbits int Bits to keep when writing (most) volumes with compression. 0->lossless floating point. Default 12 (3 significant figures)
--mass float The rough mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.
--restarget float The specified target resolution to avoid underfiltering artifacts.
--setsf str Force the structure factor to match a 'known' curve prior to postprocessing (<filename>, none). default=none
--iter int Iteration number to generate FSC filenames
--align None Will do o to e alignment and test for handedness flips. Should not be repeated as it overwrites the odd file with the aligned result.
--tomo None Modifies settings to be more appropriate for typical subtomogram averaging
--tophat str 'global', 'local' or 'localwiener'. Overall Wiener filter disabled, and replaced by a tophat filter either across the map at 0.143 as Relion appears to do, or locally based on e2fsc_local_real.py results (either local tophat or local wiener)
--ampcorrect None Will perform amplitude correction via the specified method. The default choice is strucfac.
--ncmult float Specify how much to multiply noise cutoff during flattening amplitude correction. Default is 1.05.
--localsize float Override the automatic local region size (in A) used for local resolution calculation and filtration.
--m3dpostprocess str Default=none. An arbitrary post-processor to run after all other automatic processing.
--ppid int Set the PID of the parent process, used for cross platform PPID
--automaskexpand int Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Only used if automask3d not specified.
--automask3d str Default=auto. Specify as a processor, eg - mask.auto3d:threshold=1.1:radius=30:nshells=5:nshellsgauss=5.
--mask str specify a density map file to use as mask. overwrites automask3d
--mergelowres float merge low resolution information of the two subset.
--automask3d2 str Default=None. Specify as a processor. This will be applied to the mask produced by the first automask.
--underfilter None This will shift the computed Wiener filter to be about 10%% more resolution than has been achieved.
--sym str Symmetry so we can decide how to align the particle.
--threads int Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful