Contact map visualizer

Type	PyMOL Plugin
Download	plugins/contact_map_visualizer.py
Author(s)	Venkatramanan Krishnamani
License	-
This code has been put under version control in the project Pymol-script-repo

Introduction

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

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How to get it

Right-click in the info box in top right corner, and save as.

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Required Dependencies on Linux and Mac OS X

• Tkinter
• PIL (Python Imaging Library) and
• pygame

sudo apt-get install python-tk python-imaging python-pygame

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Installing on Linux

• Navigate to plugins > install
• Locate the downloaded contact-map-visualizer.py file in the dialogbox and select 'OK'
• Quit and Restart 'pymol'

Installing on Mac OS X

Coming soon…

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Generate Contact Map

Mean contact map of a protein trajectory generated from g_mdmat tool in the Gromacs analysis package.

• Use the command g_mdmat from Gromacs analysis package. A typical contact map looks like the figure on the right.

To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command

g_mdmat -f <protein.pdb> -s <protein.pdb> -mean contact-map.xpm

To generate a mean contact map form a protein trajectory

g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm

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Usage

• Launch PyMOL
• Navigate to Plugins > Contact Map Visualizer in PyMOL
• When the first dialog box pops up, select the contact map image like the one shown above (only .png and .jpg 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.

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Screenshot

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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.
#

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