Gyration tensor: Difference between revisions
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==Required Dependencies on Linux and Mac OS X== | ==Required Dependencies on Linux and Mac OS X== | ||
* [http://wiki.python.org/moin/TkInter Tkinter] and | * [http://wiki.python.org/moin/TkInter Tkinter] and | ||
* [http://numpy.scipy.org/ | * [http://numpy.scipy.org/ Numpy] | ||
sudo apt-get install python-tk python-numpy | sudo apt-get install python-tk python-numpy | ||
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Revision as of 19:03, 2 February 2012
Type | PyMOL Plugin |
---|---|
Download | git://github.com/VenkyKrishnamani/gyration_tensor.git |
Author(s) | Venkatramanan Krishnamani |
License | - |
This code has been put under version control in the project Pymol-script-repo |
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 git://github.com/VenkyKrishnamani/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
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.
#