Main Page

Welcome to the PyMOL Wiki!

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

To request a new account, email 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 v1.8.2 has been released on April 20, 2016. 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... SelInside selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples. Usage # find all atoms inside the box spanned by (0,0,0) and (10,10,10) # for the example PDB, 1hpv fetch 1hpv pseudoatom b1, pos=[0,0,0] pseudoatom b2, pos=[10,10,10] selInside b1 or b2 The Code <source lang="python"> import pymol from pymol import cmd, stored from random import randint def selInside(bounding_object, target="*", radius=None): """ Selects all atoms of a given target type inside some selection that acts like a bounding box. PARAMS: bounding_object -- [PyMOL object/selection] the object/selection inside of which we want to choose atoms target -- [PyMOL selection] that defines the atoms to select. Use "solvent" to select only solvent atoms inside the selection radius -- [float] expand the box by this many angstroms on all sides RETURNS: (string) name of the selection created ..→

A Random PyMOL-generated Cover. See Covers.