Difference between revisions of "Main Page"

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(poll protein/nucleic)
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
! Poll
! Selection keywords
| [https://goo.gl/forms/r0Ck03VTytZQxN4A2 New protein/nucleic selection keywords for PyMOL] - Tell us what you think!
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
! Official Release
! Official Release

Revision as of 12:30, 7 February 2018

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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Official Release PyMOL v2.0 has been released on September 20, 2017.
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release PyMOL v1.8.6 has been released on March 9, 2017.
Official Release PyMOL v1.8.4 has been released on October 4, 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...


Type Python Script
Download draw_rotation_axis.py
Author(s) Pablo Guardado Calvo
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. It's very useful for drawing the axes of rotational symmetry in an oligomeric assembly.

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 ..→

A Random PyMOL-generated Cover. See Covers.