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! Official Release
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMO v1.7 have all been released] today, January 14, 2014.
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
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! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
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! New Plugin
! New Plugin

Revision as of 09:57, 8 August 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 v1.7.2 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...

Rms

Rms computes a RMS fit between two atom selections, but does not tranform the models after performing the fit.

USAGE

rms (selection), (target-selection)

EXAMPLES

fit ( mutant and name ca ), ( wildtype and name ca )

USER COMMENTS

To determine the RMS without any fitting, see Rms_Cur

Fit, Rms, Rms_Cur are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.
PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,

rms_cur A, D

won't work, due to the aforementioned reason. To fix this, one ..→

A Random PyMOL-generated Cover. See Covers.