Main Page

From PyMOLWiki
Jump to: navigation, search
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
Official Release PyMOL v1.8.2 has been released on April 20, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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...

RotationAxis

Type Python Script
Download draw_rotation_axis.py
Author(s) Pablo Guardado Calvo
License
This code has been put under version control in the project Pymol-script-repo

This script will draw a CGO cylinder representing a rotation axis for a given transformation.

The idea is to align two molecules/domains/chains/selections (using cmd.super) and extract the trasformation (TTT) matrix (T). The direction of the rotation axis, and a point are obtained from T and are used to create a cgo object representing the axis. The script generates two measures: one in the graphical screen (the rotation axis value, and the norm of the translation vector along the rotation axis) and some basic information in the command-line (the transformation matrix, the rotation angle, distance between centroids, and some pml lines that you can use to reproduce the axis...)

As always with these type of things, you have to use it at your own risk. I did not try all possible combinations, but if you find a bug, do not hesitate to contact me (pablo.guardado@gmail.com) or try to modify the code ..→

A Random PyMOL-generated Cover. See Covers.