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PMV

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 AT scripps DOT edu>.

This manual page was written by Steffen Moeller <moeller AT debian DOT org>, for the Debian project (but may be used by others).

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