Contact map visualizer: Difference between revisions
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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 [http://www.gromacs.org gromacs] package. | |||
==== | == Usage == | ||
contact_map_visualizer [ image_file [, selection ]] | |||
== Required Dependencies == | |||
* [http://pygame.org/ pygame] | * [http://pygame.org/ pygame] | ||
* [http://wiki.python.org/moin/TkInter Tkinter] (optional and usually included with PyMOL) | |||
* [http://www.pythonware.com/products/pil/ PIL] (optional, for automatically converting XPM images) | |||
Example for installing all dependencies on a Ubuntu like system: | |||
<source lang="bash"> | |||
sudo apt-get install python-tk python-imaging python-pygame | |||
</source> | |||
== | == Installation == | ||
* Navigate to plugins > install | * Navigate to plugins > install | ||
* Locate the downloaded | * Locate the downloaded '''contact_map_visualizer.py''' file in the dialogbox and select 'OK' | ||
* Quit and Restart 'pymol' | * Quit and Restart 'pymol' | ||
Alternative way: Just [[run]] the script, it will provide a command but no menu plugin entry. | |||
== Generate Contact Map == | |||
[[File:Contact-Map-of-a-Trajectory.png|thumb|200px|right|Mean contact map of a protein trajectory generated from g_mdmat tool in the Gromacs analysis package.]] | [[File:Contact-Map-of-a-Trajectory.png|thumb|200px|right|Mean contact map of a protein trajectory generated from g_mdmat tool in the Gromacs analysis package.]] | ||
Use the command [http://manual.gromacs.org/online/g_mdmat.html g_mdmat] from [http://www.gromacs.org 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 | To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command | ||
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g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm | g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm | ||
== Screenshot == | |||
[[File:Screenshot.png|thumb|800px|center]] | [[File:Screenshot.png|thumb|800px|center]] | ||
== Copyright == | == Copyright == | ||
<source lang= | <source lang="text"> | ||
# Copyright Notice | # Copyright Notice | ||
# ================ | # ================ | ||
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# | # | ||
</source> | </source> | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:Pymol-script-repo]] | [[Category:Pymol-script-repo]] | ||
Revision as of 04:16, 22 March 2012
| 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 | |
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.
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.
#