Main Page

hosted by

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 Official Release PyMOL v3.0 has been released on March 12, 2024. New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models Official Release PyMOL v2.5 has been released on May 10, 2021. Python 3 New Python 3 compatibility guide for scripts and plugins POSF New PyMOL fellowship announced for 2022-2023 Tutorial Plugins Tutorial updated for PyQt5 New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll! Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons 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 needs ..→

A Random PyMOL-generated Cover. See Covers.