Main Page

Welcome to the PyMOL Wiki!

The community-run support site for the PyMOL molecular viewer.

For Educational downloads go to http://pymol.org/educational

Quick Links

Tutorials	Table of Contents	Commands
Script Library	Plugins	FAQ
Gallery | Covers	PyMOL Cheat Sheet (PDF)	GoogleSearch

News & Updates New Script ColorByDisplacement Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins. New Script DisplacementMap Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections. New Script Two new scripts: AAindex and Sidechaincenters New Plugin CAVER_2.0 update to the CAVER plugin. New Script AngleBetweenHelices calculates the angle between two helices. Search GoogleSearch widget fixed. New Script Spectrumany creates color gradients with arbitrary color sequences. New Script BbPlane will draw CGO planes across the backbone highlighting planarity of arrangement. New Script Center Of Mass has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). New Script Jump is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL. New Scripts ResDe is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures. New Script See BiologicalUnit, for a workaround to the buggy Symexp command or if you just want to learn more about symmetry expansion in PyMOL. New Script See Supercell, the new script for making XxYxZ supercells. New Script See Split_Object_Along_Axis, for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond. New Script See Consistent_View/_Map_Inspect, which is a toolkit for rapidly inspecting multiple maps and models. Server updates The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A deep thanks to BitGnome for donating time and hardware for the PyMOL project. fetch_host setting Fetch_Host has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice. Fetch Fetch has been updated to also load electron density maps. Schrodinger Buys PyMOL Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the sale. User Movie One of our users has posted another interesting movie, images from which were created with PyMOL. New setting surface_cavity_mode to change how PyMOL displays cavities. Search fixed. Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems. New Command Cache—stores information on structures, so we don't have to recompute them. Warren News about Warren DeLano's passing may be read on Warren's memorial page. Setting Fetch_Path—Sets the default path for the fetch command. New Script SelInside—Creates a custom selection of all atoms spatially inside some user-defined box.

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 === ..→

A Random PyMOL-generated Cover. See Covers.