runPmv - Online in the Cloud

PROGRAM:

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

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