This is the command runPmv that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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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