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 | |
Enhanced version of this plugin is now available at CMPyMOL
The contact map visualizer plugin can link contact map images to the residues in PyMOL in a interactive way. Contact maps are pixel graphics where each protein residue corresponds to one line and one row of pixels. Thus for a 100 residue protein, such a image has 100x100 pixels. A common tool to generate such images is g_mdmat from the gromacs package.
Contents |
Usage
contact_map_visualizer [ image_file [, selection ]]
Required Dependencies
- pygame
- Tkinter (optional and usually included with PyMOL)
- PIL (optional, for automatically converting XPM images)
Example for installing all dependencies on a Ubuntu like system:
sudo apt-get install python-tk python-imaging python-pygame
Installation
- Navigate to plugins > install
- Locate the downloaded contact_map_visualizer.py file in the dialogbox and select 'OK'
- Quit and Restart 'pymol'
Alternative way: Just run the script, it will provide a command but no menu plugin entry.
Generate Contact Map
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
Screenshot
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. #
