Gyration tensor
From PyMOLWiki
| Type | PyMOL Plugin |
|---|---|
| Download | http://emptyewer.github.io/Gyration_tensor |
| Author(s) | Venkatramanan Krishnamani |
| License | - |
Contents |
Introduction
This program calculates and visualizes the gration tensors of a protein (based on geometry) for each chain in the PDB file.
How to get it
git clone https://github.com/emptyewer/Gyration_tensor.git
Required Dependencies on Linux and Mac OS X
sudo apt-get install python-tk python-numpy
Installing on Linux
- Navigate to plugins > install
- Locate the downloaded gyration_tensor.py file in the dialogbox and select 'OK'
- Quit and Restart 'pymol'
Usage
- Launch PyMOL
- Navigate to Plugins > Contact Map Visualizer in PyMOL
- When the first dialog box pops up, select PDB file and select 'OK'.
- The plugin calculates and outputs the Magnitude and Direction of the tensors in the debug window and draws the corresponding tensors as a cgo object in the PyMOL opengl window.
Screenshot
Requests for features are welcome
Please see your user account User:Venky.
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 Gyration Tensor 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. #
