e2segment3d

usage: prog <input volume> [options] 
	This program provides access to various algorithms for segmenting a 3-D volume into multiple pieces automatically.
	Note that you MUST have sufficient RAM to hold at least two copies of the volume in memory. Some segmentation algorithms
	may require more. The actual segmentation is performed using one of the segment.* processors. 'e2help.py processor segment'
	for more information (-v 1 will give even more).

Option	Type	Description
--version	None	show program's version number and exit
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--process	str	The name and parameters of a processor to perform the segmentation. 'e2help.py processor segment -v 1' for a full list. Default=segment.kmeans:ampweight=1:nseg=50:thr=0.8
--output	str	Name of output file for segmentation map
--mask	str	A mask to be used in segmentaion, specific use varies with segmentation method
--segout	str	Output stack for individual segmented volumes
--chimeraout	str	Name of file to write center of segments in UCSF Chimera marker format.
--pdbout	str	Name of file to write center of segments in PDB format.
--txtout	str	Name of file to write center of segments in text format (n\tx\ty\tz, with coordinates in pixels, 0,0,0 in the corner)
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--shifttocenter	None	Shift the output pdb to center of the density map
--helixfile	str	Start with existing secondary structure.
--edgefile	str	Write an edge file for pathwalker.py. Only avaliable while using existing secondary structures.
--sym	str	Symmetry of the target complex. Note the number of segment is per unit.
--asymunit	None	Write points of only one asymmetrical unit.