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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 2, 2014.
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released] on December 3, 2014.
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! New Plugin
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Revision as of 19:42, 3 December 2014

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) GoogleSearch
News & Updates
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 3, 2014.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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 v1.7.2 have all been released on August 4, 2014.
Official Release PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014.
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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...

Extra fit

extra_fit aligns multiple objects to a reference object.

New in PyMOL 1.7.2

It can use any of PyMOL's pairwise alignment methods (align, super, cealign, fit...). More precisely it can use any function which takes arguments mobile and target, so it will for example also work with tmalign. Additional keyword arguments are passed to the used method, so you can for example adjust outlier cutoff or create an alignment object.

There are several similar commands/scripts for this job, like "A > align > all to this" from the PyMOL panel, the "alignto" command, align_all.py and super_all.py scripts from Robert Campbell.

Usage

extra_fit [ selection [, reference [, method ]]]

Example

This will align 4 structures on CA atoms using the super method. It will also create an alignment object.

<syntaxhighlight lang="python"> fetch 1e4y 1ake 4ake 3hpq, async=0 remove not chain A

extra_fit name CA, 1ake, super, object=aln_super </ ..→

A Random PyMOL-generated Cover. See Covers.