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)