Main Page

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
New accounts: email jason (dot) vertrees (@) gmail dot com

News & Updates
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...
Rms cur rms_cur computes the RMS difference between two atom selections without performing any fitting. By default, only matching atoms in both selections will be used for the fit (same chain, residue number, atoms names etc.). Alternate location mess up the match! Usage rms_cur mobile, target [, mobile_state [, target_state [, quiet [, matchmaker [, cutoff [, cycles [, object ]]]]]]] Arguments See fit. Examples Example 1: Identical Identifiers Alternate location mess up the match, so remove them first. fetch 1p36 1kw7, async=0 remove not alt ""+"A" rms_cur 1p36, 1kw7 Example 2: Homologues Use align or super to create an alignment object (without fitting) and then use the alignment object in the atom selection and turn off identifier matching with matchmaker=-1. fetch 1oky 1t46, async=0 # create alignment object align 1oky, 1t46, cycles=0, transform=0, object=aln # RMSD of alignment object rms_cur 1oky & aln, 1t46 & aln, matchmaker=-1 See Also ..→

A Random PyMOL-generated Cover. See Covers.

Usage