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Contact map visualizer

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Revision as of 08:49, 13 January 2012 by Venky (talk | contribs)
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Type PyMOL Plugin
Download
Author(s) Venkatramanan Krishanamni
License -

Introduction

It is a fast and easy way of mapping contact maps to the residues in PyMOL.


How to get it

git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git

Required Dependencies on Linux and Mac OS X


Installing on Linux

  • Follow the steps below
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
cd Contact-Map-Visualizer
  • Run 'pymol' as an administrator from the command line
  • Navigate to plugins > install
  • Choose Contact-Map-Visualizer.py from the dialogbox and 'OK'
  • Quit and Restart 'pymol' (not required to be administator mode)

Installing on Mac OS X

Coming soon…


Usage

  • Launch PyMOL
  • Navigate to Plugins > Contact Map Visualizer in PyMOL
  • When the first dialog box pops up, select the contact map image (only .png and .gif are supported currently) and select 'OK'
  • In the second dialog box, select the pdb file which was used to generate the above contact map OR first/any single frame of a trajectory in pdb/mol format.
  • Once the visualizer launches, click on the location you want to visualize on the contact map, this will be reflected as selected residues in the PyMOL window.
  • Everytime a location to be visualized is selected, an image is saved in the working directory (1 file is generated for every run)

Requests for features are welcome


Copyright

# Copyright Notice
# ================
# 
# The PyMOL Plugin source code in this file is copyrighted, but you are
# free to use and copy it as long as you don't change or remove any of
# the copyright notices.
# 
# -----------------------------------------------------------------------------------
# This PyMOL Plugin Contact Maps Visualizer is
# Copyright (C) 2012 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
# 
#                        All Rights Reserved
# 
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee is hereby granted, provided that the above copyright
# notice appear in all copies and that both the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
# 
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
# PERFORMANCE OF THIS SOFTWARE.
#