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Revision as of 06:32, 11 January 2016

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News See Older News.
Did you know...

Gyration tensor

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 ..→
A Random PyMOL-generated Cover. See Covers.


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