PyMOL Wiki - User contributions [en]

CMPyMOL

2013-05-21T19:55:06Z

Venky:

{{Infobox script-repo
|type = Software
|download = http://emptyewer.github.io/CMPyMOL/
|version = 1.0b
|author = [[User:Venky|Venkatramanan Krishnamani]]
|license = The MIT License (MIT)
}}

CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.

== Website ==

http://emptyewer.github.io/CMPyMOL/

== Version History ==

* Added support for reading multi-model PDB files. (Multi-Model PDB file for NMR structure or Trajectory from MD simulations.)
* Supports displaying variance of contact points from a series of contact maps generated from multi-model PDB files.
* CMPyMOL stores the calculated contact maps, heat maps and contact density information in a local SQLite database for fast and easy subsequent access.
* Cleaner GUI.
* Parallelized the code for contact map calculation for multi-frame PDB files.

== Prerequisites ==

* Python 2.7
* Python module dependency
** [http://www.wxpython.org wxpython]
** [http://matplotlib.org matplotlib]
** [http://www.pythonware.com/products/pil/ python imaging library (PIL)]
** [http://www.numpy.org numpy]
* PyMOL. (It is recommended that the user add the PyMOL installation directory to the $PATH environment variable.)
* Stride secondary structure assignment tool. This program can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and compiled into a stand-alone executable. It is recommended that the Stride executable or its installation directory is added to the $PATH environment variable. NOTE: If this executable is not detected in the $PATH variable, the secondary structure calculation will be disabled in CMPyMOL.

=== Mac OS X ===

* Users can install the python libraries using "easy_install" or "pip". It is recommended that the user use Enthought Canopy python distribution and management package downloaded from https://www.enthought.com/products/canopy/. This package includes a robust python library management software and a python IDE.
* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into the $PATH environment variable.

=== Linux ===
* The python dependencies and PyMOL can be installed using apt-get (aptitude) or a similar package management system.

== Installation ==

There is no need for installation of the script. Optionally, a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" package, depending on the users operating system.

== Usage ==

<source lang="bash">
python /<path to CMPyMOL directory>/CMPyMOL.py
</source>

* This command will automatically invoke the PyMOL executable and the user is led through the rest of the program with a series of pop-up windows.

== Software ==

Clicking (left) and dragging a selection of contact points on the displayed contact map will highlight the corresponding residues in the PyMOL window (as red and blue colored atoms in spheres representation). In addition, several structural/biochemical properties can be overlaid on top of the contact map. The contact-map data can also be plotted in other representations. The calculated contact-map, heat-map and contact density information is stored in a local SQL database. Any subsequent access of the same PDB with matching parameters will be read from the database for fast access. The code for calculating contact map for trajectory files is parallelized for efficiency.

=== Inputs ===
* Single-frame PDB files (local)
* Multi-frame PDB trajectory files (local)
* Multi-frame trajectory files should have the following format.

<source lang="bash">
MODEL X
.
.
.
ATOM ...
ATOM ...
.
.
.
ENDMDL
</source>

NOTE: The PDB can include REMARKS, CRYST and other standard PDB information entries. The MODEL line is essential for the software to work properly (ENDMDL is optional).

=== Overlays ===
* Secondary structure of the protein is overlaid as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not found in the system path ($PATH). (Button: Secondary Structure)
* Contact points where a Charge-Charge interaction occurs are highlighted. (Button: Charged Interactions)
* Residues that interact via hydrophobic interaction are highlighted. (Button: Hydrophobic Interactions)
* Contact regions that have a B-factor that is higher than a certain cutoff are highlighted (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
* Highlights a contact point/region where the pair of selected residues are in contact (selected by checking the checkboxes). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)

=== Plots ===
* Pairwise Heat Map - Plots a 20x20 matrix of pairwise aminoacid interaction count.
* Contacts Histogram - Plots the number of contacts around a given residue. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the displays the variance contact map starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions in a protein.

=== Word of Caution ===
When using a multi-frame PDB file, the contact-map for the next frame(s) are being pre-calculated in the background (depending on the number of free CPU cores available). Clicking on "Next Frame" in rapid succession may lead to undesired results and/or a crash.

In the event of a crash, delete the database that is created in the working directory and relaunch the program.

== Requests and Disclaimer ==

Users are welcome to send me an email to request the addition of a specific feature or to report a bug.

== Main Window ==

[[File:CMPyMOL.PNG|thumb|877px|center]]

== Pairwise Aminoacid Heatmap ==
[[File:Heatmap-CMPyMOL.PNG|thumb|877px|center]]

== License ==
<source lang="text">
# The MIT License (MIT)
# =======================
#
# 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.
#
# -----------------------------------------------------------------------------------
# CMPyMOL
# Copyright (C) 2013 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this
# software and associated documentation files (the "Software"), to deal in the Software
# without restriction, including without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies
# or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
# PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
</source>

[[Category:Plugins]]
[[Category:Script_Library]]

CMPyMOL

2013-05-21T19:53:53Z

Venky: /* Screenshot */

{{Infobox script-repo
|type = Software
|download = http://emptyewer.github.io/CMPyMOL/
|version = 1.0b
|author = [[User:Venky|Venkatramanan Krishnamani]]
|license = The MIT License (MIT)
}}

CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.

== Website ==

http://emptyewer.github.io/CMPyMOL/

== Version History ==

* Added support for reading multi-model PDB files. (Multi-Model PDB file for NMR structure or Trajectory from MD simulations.)
* Supports displaying variance of contact points from a series of contact maps generated from multi-model PDB files.
* CMPyMOL stores the calculated contact maps, heat maps and contact density information in a local SQLite database for fast and easy subsequent access.
* Cleaner GUI.
* Parallelized the code for contact map calculation for multi-frame PDB files.

== Prerequisites ==

* Python 2.7
* Python module dependency
** [http://www.wxpython.org wxpython]
** [http://matplotlib.org matplotlib]
** [http://www.pythonware.com/products/pil/ python imaging library (PIL)]
** [http://www.numpy.org numpy]
* PyMOL. (It is recommended that the user add the PyMOL installation directory to the $PATH environment variable.)
* Stride secondary structure assignment tool. This program can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and compiled into a stand-alone executable. It is recommended that the Stride executable or its installation directory is added to the $PATH environment variable. NOTE: If this executable is not detected in the $PATH variable, the secondary structure calculation will be disabled in CMPyMOL.

=== Mac OS X ===

* Users can install the python libraries using "easy_install" or "pip". It is recommended that the user use Enthought Canopy python distribution and management package downloaded from https://www.enthought.com/products/canopy/. This package includes a robust python library management software and a python IDE.
* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into the $PATH environment variable.

=== Linux ===
* The python dependencies and PyMOL can be installed using apt-get (aptitude) or a similar package management system.

== Installation ==

There is no need for installation of the script. Optionally, a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" package, depending on the users operating system.

== Usage ==

<source lang="bash">
python /<path to CMPyMOL directory>/CMPyMOL.py
</source>

* This command will automatically invoke the PyMOL executable and the user is led through the rest of the program with a series of pop-up windows.

== Software ==

Clicking (left) and dragging a selection of contact points on the displayed contact map will highlight the corresponding residues in the PyMOL window (as red and blue colored atoms in spheres representation). In addition, several structural/biochemical properties can be overlaid on top of the contact map. The contact-map data can also be plotted in other representations. The calculated contact-map, heat-map and contact density information is stored in a local SQL database. Any subsequent access of the same PDB with matching parameters will be read from the database for fast access. The code for calculating contact map for trajectory files is parallelized for efficiency.

=== Inputs ===
* Single-frame PDB files (local)
* Multi-frame PDB trajectory files (local)
* Multi-frame trajectory files should have the following format.

<source lang="bash">
MODEL X
.
.
.
ATOM ...
ATOM ...
.
.
.
ENDMDL
</source>

NOTE: The PDB can include REMARKS, CRYST and other standard PDB information entries. The MODEL line is essential for the software to work properly (ENDMDL is optional).

=== Overlays ===
* Secondary structure of the protein is overlaid as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not found in the system path ($PATH). (Button: Secondary Structure)
* Contact points where a Charge-Charge interaction occurs are highlighted. (Button: Charged Interactions)
* Residues that interact via hydrophobic interaction are highlighted. (Button: Hydrophobic Interactions)
* Contact regions that have a B-factor that is higher than a certain cutoff are highlighted (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
* Highlights a contact point/region where the pair of selected residues are in contact (selected by checking the checkboxes). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)

=== Plots ===
* Pairwise Heat Map - Plots a 20x20 matrix of pairwise aminoacid interaction count.
* Contacts Histogram - Plots the number of contacts around a given residue. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the displays the variance contact map starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions in a protein.

=== Word of Caution ===
When using a multi-frame PDB file, the contact-map for the next frame(s) are being pre-calculated in the background (depending on the number of free CPU cores available). Clicking on "Next Frame" in rapid succession may lead to undesired results and/or a crash.

In the event of a crash, delete the database that is created in the working directory and relaunch the program.

== Requests and Disclaimer ==

Users are welcome to send me an email to request the addition of a specific feature or to report a bug.

== Main Window ==

[[File:CMPyMOL.PNG|thumb|877px|center]]

== License ==
<source lang="text">
# The MIT License (MIT)
# =======================
#
# 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.
#
# -----------------------------------------------------------------------------------
# CMPyMOL
# Copyright (C) 2013 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this
# software and associated documentation files (the "Software"), to deal in the Software
# without restriction, including without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies
# or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
# PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
</source>

[[Category:Plugins]]
[[Category:Script_Library]]

2013-05-20T20:38:23Z

Venky: /* Screenshot */

{{Infobox script-repo
|type = Software
|download = http://emptyewer.github.io/CMPyMOL/
|version = 1.0b
|author = [[User:Venky|Venkatramanan Krishnamani]]
|license = The MIT License (MIT)
}}

CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the 3D visualization capabilities of PyMOL and 2D protein contact maps with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.

== Website ==

http://emptyewer.github.io/CMPyMOL/

== Prerequisites ==

* Python 2.7
* Python module dependency
** [http://www.wxpython.org wxpython]
** [http://matplotlib.org matplotlib]
** [http://www.pythonware.com/products/pil/ python imaging library (PIL)]
** [http://www.numpy.org numpy]
* PyMOL executable. It is recommended that the user make sure the directory of installed executable is listed in the $PATH variable.
* Stride executable. This can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and easily compiled into an executable. It is recommemded that the executable or its directory is listed in the system variable $PATH. NOTE: If this executable is not installed properly, the secondary structure calculation will be automatically disabled.

=== Mac OS X ===

* Users can install the python libraries using "easy_install" or "pip". It is recommened that the user downloads Enthough Canopy python distribution and management package from https://www.enthought.com/products/canopy/. This package includes a robust python library management software and a python IDE.
* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into $PATH.

=== Linux ===
* The python dependencies and PyMOL can be installed using apt-get (aptitude) or similar package management system.

== Installation ==

There is no need for installation of the script. Optionally, a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" packages depending on the users operating system.

== Usage ==

<source lang="bash">
python CMPyMOL.py
</source>

* This command will automatically invoke the PyMOL executable and the user is led through the rest of the program with a series of pop-up windows.

== Software ==

Clicking (left) and draging a selection of points on the displayed contact map will highlight the corresponding residues involved in that contact in the PyMOL window (as red and blue colored spheres). In addition, several structural/biochemical properties can be overlayed on top of the contact map (listed below). The contact-map data can also be plotted in other representations.

=== Overlays ===
* Secondary structure of the protein as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not installed. (Button: Secondary Structure)
* Contact points where a Charge-Charge interaction occurs. (Button: Charged Interactions)
* Residues that interact via hydrophobic interaction. (Button: Hydrophobic Interactions)
* Contact regions that have a b-factor that is higher than a certain cutoff (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
* Highlights a contact point/region where the selected pair of residues are in contact (selected by checking the checkbox). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)

=== Plots ===
* Pairwise Heat Map - Plots a 20x20 matrix of count of pairwise aminoacid interactions.
* Contacts Histogram - Plots the number of contacts formed by a given residue as a bar graph. Selecting a particular bar highlights the corresponding residue in the PyMOL window.

== Requests and Disclaimer ==

Users are welcome to send me an email to request the addition of a specific feature. I am actively developing this software.

== Screenshot ==

[[File:CMPyMOL.PNG|thumb|877px|center]]

== License ==
<source lang="text">
# The MIT License (MIT)
# =======================
#
# 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.
#
# -----------------------------------------------------------------------------------
# CMPyMOL
# Copyright (C) 2013 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this
# software and associated documentation files (the "Software"), to deal in the Software
# without restriction, including without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies
# or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
# PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
</source>

[[Category:Plugins]]
[[Category:Script_Library]]

2013-05-01T17:17:46Z

Venky:

2013-04-30T18:53:14Z

Venky:

{{Infobox script-repo
|type = Software
|download = https://github.com/VenkyKrishnamani/CMPyMOL
|author = [[User:Venky|Venkatramanan Krishnamani]]
|license = The MIT License (MIT)
}}

CMPyMOL combines the 3D visualization capabilities of PyMol and protein contact map into a rich and intuitive tool for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.

== Prerequisites ==

* Python 2.7
* Python framework dependency
** [http://matplotlib.org matplotlib]
** [http://www.pythonware.com/products/pil/ python imaging library (PIL)]
** [http://www.numpy.org numpy]
** [http://biopython.org/wiki/Main_Page biopython]
* PyMOL executable. It is recommended that the user make sure the directory of installed executable is listed in the $PATH variable.
* Stride executable. This can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and easily compiled into an executable. It is recommemded that the executable or its directory is listed in the system variable $PATH. NOTE: If this executable is not installed properly, the secondary structure calculation will be automatically disabled.

=== Mac OS X ===

* Users can install the python dependencies easily using "easy_install" or "pip". It is recommened that the user downloads Enthough Canopy python distribution and management package from https://www.enthought.com/products/canopy/. It comes with a robust package management software and a python IDE.
* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. This automatically adds the executable into $PATH.

=== Linux ===
* The python dependencies and PyMOL can be installed using apt-get (aptitude) or similar package management system.

== Installation ==

There is no installation of the script is required required. Optionally a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" packages depending on the users operating system.

== Usage ==

<source lang="bash">
python CMPyMOL.py
</source>

* The above command will automatically invoke PyMOL. The user is led through the rest of the program with a series of pop-up window.

== Software ==

Left-clicking and draging anywhere on the contact map displayed will highlight the corresponding residues in PyMOL (spheres). In addition, there are several different structural/biochemical properties overlays that can be overlayed on top of the contact map. The user can plot the contact-map data in other representations.

=== Overlays ===
* Secondary Structure of the protein as strips of color (Secondary Structure). This button won't be active if secondary structure calculation program stride is not installed.
* Contact regions where a Charge-Charge interaction occurs (Charged Interactions)
* Residues that interact via a hydrophobic interaction (Hydrophobic Interactions)
* Contact regions that have a b-factor that is higher than a certain cutoff (B-factor). The cutoff can be varied using a slider (slider below the button).
* Highlights a contact point/region where a pair of residues are in contact. If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another on of the same type is highlighted.

=== Plots ===
* Pairwise Heat Map - Plots a 20x20 matrix of number of pairwise aminoacid interactions as a colored heatmap.
* Contacts Histogram - Plots the number of residue wise contacts of a given protein.

== Requests and Disclaimer ==

Users are welcome to send me an email to request the addition of a specific feature. I am actively developing this software. Please do understand that I have other committments, so the requested feature may not be able to implemented promptly.

== Screenshot ==

[[File:CMPyMOL-Screenshot.PNG|thumb|877px|center]]

== License ==
<source lang="text">
# The MIT License (MIT)
# =======================
#
# 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.
#
# -----------------------------------------------------------------------------------
# CMPyMOL
# Copyright (C) 2013 by Venkatramanan Krishnamani <venks@andrew.cmu.edu>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this
# software and associated documentation files (the "Software"), to deal in the Software
# without restriction, including without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies
# or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
# PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
</source>

[[Category:Plugins]]
[[Category:Script_Library]]

CMPyMOL

2013-04-30T18:52:38Z

Venky:

CMPyMOL

2013-04-30T18:51:32Z

Venky:

CMPyMOL

2013-04-30T18:50:48Z

Venky:

2012-01-13T18:44:26Z

Venky: /* Generate Contact Map */

{{Infobox script-repo
|type = plugin
|filename = plugins/contact_map_visualizer.py
|author = 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==
* [http://wiki.python.org/moin/TkInter Tkinter]
* [http://www.pythonware.com/products/pil/ PIL] (Python Imaging Library) and
* [http://pygame.org/ pygame]
sudo apt-get install python-tk 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 ===
[[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
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

----

=== 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 ===

[[File:Screenshot.png|thumb|800px|center]]
----

=== Requests for features are welcome ===

----

== Copyright ==
<source lang=bash>
# 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.
#
</source>
----

[[Category:Plugins]]

Contact map visualizer

2012-01-13T17:48:32Z

Venky:

{{Infobox script-repo
|type = plugin
|download = [https://raw.github.com/VenkyKrishnamani/Contact-Map-Visualizer/master/Contact-Map-Visualizer.py Contact-Map-Visualizer.py]
|author = Venkatramanan Krishanamni
|license = -
}}

== Introduction ==
It is a fast and easy way of mapping contact maps to the residues in PyMOL.
----

==== How to get it ====

* You can download it from the git repository https://github.com/VenkyKrishnamani/Contact-Map-Visualizer
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
----

==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
sudo apt-get install python-imaging
* [http://pygame.org/ pygame]
sudo apt-get install python-pygame
----

===Installing on Linux===

* Follow the steps below
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
cd Contact-Map-Visualizer
* Run 'pymol' as an administrator from the command line
* Navigate to plugins > install
* Choose Contact-Map-Visualizer.py from the dialogbox and 'OK'
* Quit and Restart 'pymol' (not required to be administator mode)

===Installing on Mac OS X===
Coming soon…
----
=== 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.

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 ===

[[File:Screenshot.png|thumb|800px|center]]
----

=== Requests for features are welcome ===

----

== Copyright ==
<source lang=bash>
# 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.
#
</source>
----

[[Category:Plugins]]

File:Screenshot.png

2012-01-13T17:45:38Z

Venky:

Contact map visualizer

2012-01-13T17:40:39Z

Venky: /* Generate Contact Map */

{{Infobox script-repo
|type = plugin
|download = [https://raw.github.com/VenkyKrishnamani/Contact-Map-Visualizer/master/Contact-Map-Visualizer.py Contact-Map-Visualizer.py]
|author = Venkatramanan Krishanamni
|license = -
}}

== Introduction ==
It is a fast and easy way of mapping contact maps to the residues in PyMOL.
----

==== How to get it ====

* You can download it from the git repository https://github.com/VenkyKrishnamani/Contact-Map-Visualizer
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
----

==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
sudo apt-get install python-imaging
* [http://pygame.org/ pygame]
sudo apt-get install python-pygame
----

===Installing on Linux===

* Follow the steps below
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
cd Contact-Map-Visualizer
* Run 'pymol' as an administrator from the command line
* Navigate to plugins > install
* Choose Contact-Map-Visualizer.py from the dialogbox and 'OK'
* Quit and Restart 'pymol' (not required to be administator mode)

===Installing on Mac OS X===
Coming soon…
----
=== 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.

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.
----

=== Requests for features are welcome ===

----

== Copyright ==
<source lang=bash>
# 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.
#
</source>
----

[[Category:Plugins]]

Contact map visualizer

2012-01-13T17:39:10Z

Venky:

{{Infobox script-repo
|type = plugin
|download = [https://raw.github.com/VenkyKrishnamani/Contact-Map-Visualizer/master/Contact-Map-Visualizer.py Contact-Map-Visualizer.py]
|author = Venkatramanan Krishanamni
|license = -
}}

== Introduction ==
It is a fast and easy way of mapping contact maps to the residues in PyMOL.
----

==== How to get it ====

* You can download it from the git repository https://github.com/VenkyKrishnamani/Contact-Map-Visualizer
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
----

==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
sudo apt-get install python-imaging
* [http://pygame.org/ pygame]
sudo apt-get install python-pygame
----

===Installing on Linux===

* Follow the steps below
git clone git://github.com/VenkyKrishnamani/Contact-Map-Visualizer.git
cd Contact-Map-Visualizer
* Run 'pymol' as an administrator from the command line
* Navigate to plugins > install
* Choose Contact-Map-Visualizer.py from the dialogbox and 'OK'
* Quit and Restart 'pymol' (not required to be administator mode)

===Installing on Mac OS X===
Coming soon…
----
=== Generate Contact Map ===
* 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. [[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.]]

For 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.
----

=== Requests for features are welcome ===

----

== Copyright ==
<source lang=bash>
# 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.
#
</source>
----

[[Category:Plugins]]

File:Contact-Map-of-a-Trajectory.png

2012-01-13T17:34:59Z

Venky: A Typical contact map generated from g_mdmat program in the Gromacs analysis package.

A Typical contact map generated from g_mdmat program in the Gromacs analysis package.