NAME

       adt - AutoDockTools, a graphical front-end for AutoDock

SYNOPSIS

       runAdt [options]

DESCRIPTION

       This  manual  page  is  an  almost literal translation of the output provided by runAdt -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

EXAMPLE:

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

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

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

SEE ALSO

       http://mgltools.scripps.edu, http://autodock.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                                   ADT(1)