|License||The MIT License (MIT)|
|This code has been put under version control in the project Pymol-script-repo|
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.
- Python 2.7
- Python framework 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 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.
- The python dependencies and PyMOL can be installed using apt-get (aptitude) or similar package management system.
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.
- The above command will automatically invoke PyMOL. The user is led through the rest of the program with a series of pop-up window.
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.
- 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.
- Regions where a Charge-Charge interaction occurs (Charged Interactions)
- Residues that interact by a hydrophobic interaction (Hydrophobic Interactions)
- Contact regions that have a b-factor that is higher than a certain cutoff that is fixed by a slider (B-factor and 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.
- 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.
# 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 <firstname.lastname@example.org> # # 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.