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Revision as of 09:27, 19 February 2019

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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: 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
Python 3 New Python 3 compatibility guide for scripts and plugins
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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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