Difference between revisions of "CMPyMOL"

Type	Software
Download	https://github.com/VenkyKrishnamani/CMPyMOL
Author(s)	Venkatramanan Krishnamani
License	The MIT License (MIT)

Revision as of 13:02, 1 May 2013

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.

Prerequisites

Python 2.7
Python module dependency
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

python CMPyMOL.py

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

License

#  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.

@@ Line 7: / Line 7: @@
 }}
-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.
+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.
 == Prerequisites ==
@@ Line 21: / Line 21: @@
 === 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.
+* 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 is recommended and is available from MacPorts http://www.macports.org.
+* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into $PATH.
 === Linux ===
-* The python module dependencies and PyMOL can be installed using apt-get (aptitude) or similar package management system.
+* 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.
+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 ==
@@ Line 37: / Line 37: @@
 </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.
+* 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 ==
-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.
+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 strips of color (Secondary Structure). This button won't be active if secondary structure calculation program stride is not installed.
+* 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 regions where a Charge-Charge interaction occurs (Charged Interactions)
+* Contact points where a Charge-Charge interaction occurs. (Button: Charged Interactions)
-* Residues that interact via a hydrophobic interaction (Hydrophobic Interactions)
+* Residues that interact via hydrophobic interaction. (Button: 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).
+* 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 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.
+* 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 number of pairwise aminoacid interactions as a colored heatmap.
+* Pairwise Heat Map - Plots a 20x20 matrix of count of pairwise aminoacid interactions.
-* Contacts Histogram - Plots the number of residue wise contacts of a given protein.
+* 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 ==