This program extract particles from .ali files from IMOD reconstruction. It takes most information, including XTILT angle and boundary of trimmed volume from IMOD setting and log files. So make sure the whole IMOD project is not corrupted after the reconstruction. This program is test on IMOD 4.7.13 (10/15/2014). There is no garantee that it will work on project generated by any other IMOD versions.
	Extracting particles using the box locations saved in the info file corresponding to the tomogram
	[prog] --tomo <tomogram name> --edf <imod edf file> --ptclout <output 2D particle file name> [options]
	Extracting particles using 3D particles extracted from the tomogram
	[prog] --ptclin <3D particles> --edf <imod edf file> --ptclout <output 2D particle file name> [options]

Option Type Description
--version None show program's version number and exit
--tomo str File name of reconstructed tomogram.
--ptclin str File name of input 3D particles.
--edf str IMOD .edf file name.
--ptclout str File name of output 2D extracted particles.
--unbin float Unbin factor from input particles/tomogram to raw tilt. If unspecified, the program will calculate from the Apix of the header.
--boxsz int Box size of extracted 2D particles.
--defcol int Which column of ctf file is the defocus
--weight None Weight the particles by the variance of defocus.
--ctffile str Estimated CTF