pmv(1) 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
overwrite log file
create a log file with a unique name
turn off logging
turn off Splash Screen
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 <[email protected]>.

This manual page was written by Steffen Moeller <[email protected]>, for the Debian project (but may be used by others).