Contact map visualizer - Revision history

Cchem: 1 revision

2021-12-06T03:43:03Z

1 revision

Zhentg: /* Generate Contact Map */

2021-11-17T09:34:20Z

Generate Contact Map

Pyadmin: 24 revisions

2014-03-28T02:15:14Z

24 revisions

Venky at 02:14, 1 May 2013

2013-05-01T02:14:40Z

Venky at 02:13, 1 May 2013

2013-05-01T02:13:27Z

Venky at 02:13, 1 May 2013

2013-05-01T02:13:03Z

Speleo3: updates for 2.1

2012-03-22T09:16:09Z

updates for 2.1

Tlinnet at 15:13, 15 January 2012

2012-01-15T15:13:12Z

Tlinnet at 23:31, 13 January 2012

2012-01-13T23:31:27Z

Venky at 20:29, 13 January 2012

2012-01-13T20:29:22Z

@@ Line 44: / Line 44: @@
 To generate a mean contact map form a protein trajectory
   g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm
 == Screenshot ==

@@ Line 5: / Line 5: @@
 |license   = -
 }}
 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 ==

@@ Line 8: / Line 8: @@
 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.
-'''Enhanced version of this plugin is now available at [CMPyMOL]'''
+'''Enhanced version of this plugin is now available at''' [CMPyMOL]
 == Usage ==

← Older revision		Revision as of 02:13, 1 May 2013
Line 7:		Line 7:

	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.		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.
		+
		+	'''Enhanced version of this plugin is now available at [CMPyMOL]'''

	== Usage ==		== Usage ==

@@ Line 6: / Line 6: @@
 }}
-== Introduction ==
+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.
-==== How to get it ====
+== Usage ==
-Right-click in the info box in top right corner, and save as.
-----
+ contact_map_visualizer [ image_file [, selection ]]
 * [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)
-----
+* [http://www.pythonware.com/products/pil/ PIL] (optional, for automatically converting XPM images)
-===Installing on Linux===
+== Installation ==
 * 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'
-===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.]]
-* 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
@@ Line 41: / Line 43: @@
   g_mdmat -f <trajectory.pdb> -s <starting-frame.pdb> -mean contact-map.xpm
-----
+== Screenshot ==
 [[File:Screenshot.png|thumb|800px|center]]
 == Copyright ==
-<source lang=bash>
+<source lang="text">
 # Copyright Notice
 # ================
@@ Line 93: / Line 80: @@
+#
 </source>
 [[Category:Plugins]]
 [[Category:Pymol-script-repo]]

← Older revision	Revision as of 03:43, 6 December 2021
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← Older revision	Revision as of 02:15, 28 March 2014
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← Older revision		Revision as of 15:13, 15 January 2012
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	[[Category:Plugins]]		[[Category:Plugins]]
		+	[[Category:Pymol-script-repo]]

@@ Line 2: / Line 2: @@
 |type      = plugin
 |filename = plugins/contact_map_visualizer.py
-|author    = Venkatramanan Krishnamani
+|author    = [[User:Venky|Venkatramanan Krishnamani]]
 |license   = -
 }}