e2boxer_old

usage: prog [options] <image> <image2>....

The 'new' version of e2boxer. While it is quite usable, it is still in need of some work.

For example:

e2boxer.py ????.mrc --boxsize=256

Option Type Description
--version None show program's version number and exit
--boxsize, -B int Box size in pixels
--write_dbbox None Write coordinate file (eman1 dbbox) files
--write_ptcls None Write particles to disk
--exclude_edges None Don't generate output for any particles extending outside the micrograph
--exclude_bad None Don't generate output for any particles marked as exclude
--force, -f None Force overwrite
--format None Format of the output particle images. For EMAN2 refinement must be HDF.
--norm str Normalization processor to apply to written particle images. Should be normalize, normalize.edgemean,etc.Specific "None" to turn this off
--invert None If writing outputt inverts pixel intensities
--suffix str suffix which is appended to the names of output particle and coordinate files
--dbls str data base list storage, used by the workflow. You can ignore this argument.
--autoboxer str A key of the swarm_boxers dict in the local directory, used by the workflow.
--ppid int Set the PID of the parent process, used for cross platform PPID
--gui None Dummy option; used in older version of e2boxer
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--gauss_autoboxer str Name of autoboxed file whose autoboxing parameters (obtained via some previous run of Gauss autoboxer via the GUI) should be used for automatic boxing.
--do_ctf str Name of file whose ctf estimation parameters (obtained via some previous run of Gauss autoboxer via the GUI) should be used for automatic ctf estimation.
--cter None CTF estimation using cter
--indir str Directory containing micrographs to be processed.
--nameroot str Prefix of micrographs to be processed.
--micsuffix str A string denoting micrograph type. For example 'mrc', 'hdf', 'ser' ...
--wn int Size of window to use (should be slightly larger than particle box size)
--Cs float Microscope Cs (spherical aberation)
--voltage float Microscope voltage in KV
--ac float Amplitude contrast (percentage, default=10)
--kboot int kboot
--MPI None use MPI version
--debug None debug mode
--apix float pixel size in Angstroms