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
-
AUTHOR
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).