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{{Infobox script-repo | {{Infobox script-repo | ||
|type = plugin | |type = plugin | ||
| − | |download = | + | |download = plugins contact_map_visualizer.py |
|author = Venkatramanan Krishanamni | |author = Venkatramanan Krishanamni | ||
|license = - | |license = - | ||
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==== How to get it ==== | ==== How to get it ==== | ||
| − | + | Right-click in the info box in top right corner, and save as. | |
| − | |||
| − | |||
---- | ---- | ||
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* [http://wiki.python.org/moin/TkInter Tkinter] | * [http://wiki.python.org/moin/TkInter Tkinter] | ||
* [http://www.pythonware.com/products/pil/ PIL] (Python Imaging Library) and | * [http://www.pythonware.com/products/pil/ PIL] (Python Imaging Library) and | ||
| − | |||
* [http://pygame.org/ pygame] | * [http://pygame.org/ pygame] | ||
| − | sudo apt-get install python-pygame | + | sudo apt-get install python-imaging python-pygame |
---- | ---- | ||
===Installing on Linux=== | ===Installing on Linux=== | ||
| − | |||
* Follow the steps below | * Follow the steps below | ||
| − | |||
| − | |||
| − | |||
* Navigate to plugins > install | * Navigate to plugins > install | ||
* Choose Contact-Map-Visualizer.py from the dialogbox and 'OK' | * Choose Contact-Map-Visualizer.py from the dialogbox and 'OK' | ||
| − | * Quit and Restart 'pymol' | + | * Quit and Restart 'pymol' |
===Installing on Mac OS X=== | ===Installing on Mac OS X=== | ||
| Line 39: | Line 32: | ||
=== Generate Contact Map === | === 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. | * 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. | ||
Revision as of 18:18, 13 January 2012
| Type | PyMOL Plugin |
|---|---|
| Download | plugins contact_map_visualizer.py |
| 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
Right-click in the info box in top right corner, and save as.
Required Dependencies on Linux and Mac OS X
sudo apt-get install python-imaging python-pygame
Installing on Linux
- Follow the steps below
- Navigate to plugins > install
- Choose Contact-Map-Visualizer.py from the dialogbox and 'OK'
- Quit and Restart 'pymol'
Installing on Mac OS X
Coming soon…
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
For a mean contact map for a protein trajectory
g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm
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.
Screenshot
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.
#