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Revision as of 15:52, 26 January 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
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...

Ray trace disco factor

The ray_trace_disco_factor setting has an effect on ray_trace_mode 1-3. With small values, outlines will appear at surface curvature discontinuities.
set ray_trace_disco_factor, 0.0 set ray_trace_disco_factor, 1.0
Ray trace disco factor-0-cartoon.png Ray trace disco factor-1-cartoon.png
Ray trace disco factor-0-spheres.png Ray trace disco factor-1-spheres.png
Ray trace disco factor-0-sticks.png Ray trace disco factor-1-sticks.png

Usage

set ray_trace_mode
set ray_trace_disco_factor, 1.0 ;# disable effect
set ray_trace_disco_factor, 0.1 ;# some outlines
set ray_trace_disco_factor, 0.0 ;# strong outlines

Example

# load a molecule
fragment indane
show_as spheres

# white background makes black outlines
bg_color white

# enable outline mode
set ray_trace_mode, 3
set ray_trace_disco_factor, 0.0
ray

See Also
A Random PyMOL-generated Cover. See Covers.


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