NAME
pmv - Python Molecular Viewer
SYNOPSIS
runPmv [options]
DESCRIPTION
This manual page is an almost literal translation of the output
provided by runPmv -h command.
OPTIONS
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
EXAMPLE:
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
SEE ALSO
http://mgltools.scripps.edu
AUTHOR
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).
Januar 2, 2008 PMV(1)