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

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).