Contact map visualizer: Difference between revisions

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== Introduction ==
'''Enhanced version of this plugin is now available at [[CMPyMOL]]'''
It is a fast and easy way of mapping contact maps to the residues in PyMOL.
----


==== How to get it ====
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.
Right-click in the info box in top right corner, and save as.
 
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== Usage ==
 
contact_map_visualizer [ image_file [, selection ]]
 
== Required Dependencies ==


==Required Dependencies on Linux and Mac OS X==
* [http://wiki.python.org/moin/TkInter Tkinter]
* [http://www.pythonware.com/products/pil/ PIL] (Python Imaging Library) and
* [http://pygame.org/ pygame]
* [http://pygame.org/ pygame]
sudo apt-get install python-tk python-imaging python-pygame
* [http://wiki.python.org/moin/TkInter Tkinter] (optional and usually included with PyMOL)
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* [http://www.pythonware.com/products/pil/ PIL] (optional, for automatically converting XPM images)


===Installing on Linux===
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 contact-map-visualizer.py file in the dialogbox and select 'OK'
* Locate the downloaded '''contact_map_visualizer.py''' file in the dialogbox and select 'OK'
* Quit and Restart 'pymol'
* Quit and Restart 'pymol'


===Installing on Mac OS X===
Alternative way: Just [[run]] the script, it will provide a command but no menu plugin entry.
Coming soon…
 
----
== 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.   
 


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


----
For Gromacs 2021
To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command
gmx g_mdmat -f <protein.pdb> -s <protein.pdb> -mean contact-map.xpm
To generate a mean contact map form a protein trajectory
gmx g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm
To convert XPM to PNG format
convert contact-map.xpm contact-map.png


=== Usage ===
== Screenshot ==
 
* 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 ===


[[File:Screenshot.png|thumb|800px|center]]
[[File:Screenshot.png|thumb|800px|center]]
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=== Requests for features are welcome ===
----


== Copyright ==
== Copyright ==
<source lang=bash>
<source lang="text">
# Copyright Notice
# Copyright Notice
# ================
# ================
Line 93: Line 90:
#
#
</source>
</source>
----


[[Category:Plugins]]
[[Category:Plugins]]
[[Category:Pymol-script-repo]]

Latest revision as of 04:34, 17 November 2021

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.

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

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

For Gromacs 2021 To generate contact map of a single PDB. For example contact map for a PDB from RCSB, use the following command 

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

To generate a mean contact map form a protein trajectory 

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

To convert XPM to PNG format 

convert contact-map.xpm contact-map.png

Screenshot

Screenshot.png

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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