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Revision as of 04:43, 1 May 2016

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) 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...

Ramp New

ramp_new creates a color ramp based on a map potential value or based on proximity to a molecular object.

Usage

ramp_new name, map_name [, range [, color [, state [, selection [,
       beyond [, within [, sigma [, zero ]]]]]]]]
  • name = string: name of the ramp object to create
  • map_name = string: name of the map (for potential) or molecular object (for proximity)
  • range = list: values corresponding to slots in the ramp {default: [-1, 0, 1]}
  • color = list or str: colors corresponding to slots in the ramp or a given palette name: afmhot, grayscale, object, rainbow, traditional, grayable, hot, ocean, and sludge {default: [red, white, blue]}
  • state = integer: state identifier {default: 1}
  • selection = selection: for automatic ranging (maps only) {default: }
  • with automatic ranging only:
    • beyond = number: are we excluding values beyond a certain distance from the selection? {default: 2.0}
    • within = number: are we only including valuess within a certain distance from the ..→
A Random PyMOL-generated Cover. See Covers.