pmv(1)

NAME

pmv - Python Molecular Viewer

runPmv [options]

This manual page is an almost literal translation of the output provided by runPmv -h command.

A summary of options is included below. For a complete description, refer to the tutorials and documentation that is available online.

-h, --help: Show summary of options.
-a or --again: play back lastlog file
--overwriteLog: overwrite log file
--uniqueLog: create a log file with a unique name
--noLog: turn off logging
--noSplash: turn off Splash Screen
--die do not start GUI event loop
--customizer file: run the user specified file
--lib packageName: add a libraries of commands
-v r, --vision run: run vision networks on the command line
-v o, --vision once: run vision networks and exit ADT
-d or --dmode modes: specify a display mode; modes can be any a combination of display mode
'cpk' : cpk
'lines': lines
'ss' : secondary structure ribbon
'sb' : sticks and balls
'lic' : licorice
'ms' : molecular surface
'ca' : C-alpha trace
'bt' : backbone trace
'sp' : CA-spline
'sssb' : secondary structure for proteins, sticks and balls for; other residues with bonds lines for other residues without bonds
-c or --cmode modes: specify a dispaly mode color scheme:
'ca' : color by atom
'cr' : color by residue (RASMOL scheme)
'cc' : color by chain
'cm' : color by molecule
'cdg': color using David Goodsell's scheme
'cs' : color residues using Shapely scheme
'css': color by secondary structure element
--update [nightly|tested|clear]: Updates MGLTools. If no arguments are given then the Update Manager GUI is provided
'nightly': download and install Nightly Builds
'tested' : download and install tested Nightly Builds
'clear' : clear/uninstall all the updates

display protein as ribbon, non protein as sticks and balls and color by atom type

pmv -i --dmode sssb --cmode cr myprot.pdb

pmv -i -m sssb -c cr myprot.pdb

AutoDockTools was written by researchers of the Molecular Graphics Lab at the Scripps Institute <mgltools@scripps.edu>.

This manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but may be used by others).