Gyration tensor: Difference between revisions
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{{Infobox script-repo | {{Infobox script-repo | ||
|type = plugin | |type = plugin | ||
| | |download = http://emptyewer.github.io/Gyration_tensor | ||
|author = [[User:Venky|Venkatramanan Krishnamani]] | |author = [[User:Venky|Venkatramanan Krishnamani]] | ||
|license = - | |license = - | ||
| Line 11: | Line 11: | ||
==== How to get it ==== | ==== How to get it ==== | ||
git clone | git clone https://github.com/emptyewer/Gyration_tensor.git | ||
---- | ---- | ||
==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 | ||
---- | ---- | ||
| Line 40: | Line 40: | ||
=== Requests for features are welcome === | === Requests for features are welcome === | ||
Please see your user account [[User:Venky]]. | |||
---- | ---- | ||
Latest revision as of 11:12, 2 May 2013
| Type | PyMOL Plugin |
|---|---|
| Download | http://emptyewer.github.io/Gyration_tensor |
| Author(s) | Venkatramanan Krishnamani |
| License | - |
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.
#