e2boxadjust

usage: prog [options] <sets/file.lst> <classmx_xx.hdf> <box3d 1> <box3d 2> ...

This program is part of a pipeline to improve centering of subtomograms prior to alignment and averaging.
This is a typical workflow:

1) select 3-D particles and store locations in .box3d files with names agreeing with the name of the tomogram, eg
  rawtomograms/file0001.hdf -> rawtomograms/file0001.box3d

2) extract the 3-D particles from the tomograms, and generate Z-projections corresponding to each particle (this may be done automatically by e2spt_boxer)

3) insure that the Z-projections are normalized, filtered and have postive (white) contrast against the background, eg:
  e2proc2d.py spt_particles/file0001_prjsz.hdf spt_particles/file0001_prjsz.hdf --inplace --process filter.lowpass.gauss:cutoff_abs=0.1 --process filter.highpass.gauss:cutoff_abs=0.02 --mult -1 --process normalize.edgemean

4) build a set containing all of the z projection stacks, eg
  e2proclst.py spt_particles/file0001_prjsz.hdf spt_particles/file0002_prjsz.hdf --create sets/all_prjsz.lst

5) run e2refine2d.py

6) run this program, eg
  e2boxadjust.py sets/all_prjsz.lst r2d_01/classmx_08.hdf rawtomograms/*box3d -v 2

7) re-extract the particles using the new _cen.box3d files