Dienstag, 13. Mai 2014

Illustrating protein structures

PyMOL can produce really nice protein structures.
Bacillus circulans xylanase with bound substrate (center).
This rendering uses ambient occlusion. The imporant settings are

set light_count, 10
set spec_count, 1
set shininess, 10
set sphecular, 0.25
set ambient, 0
set direct, 0
set reflect, 1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue

What seems a bit tricky to get are the black outlines and depends on the background color setting.
The following command sequence seems to work, assuming the background is white when you start PyMOL.

1) set ray_trace_mode, 1 (color + outlines)
2) ray (outlines will be white)
3) bg black
4) ray (outlines will be white)
5) bg white
6) ray (outlines should be black)

This swapping of background is most likely not needed if you want to plot to a black background. I'm using PyMOL 1.3 and it could also be different in other versions.

If you use these instructions in your work, please be kind enough to credit this blog post.


  1. Nice! Can you also control the thickness of the mourning edges?

    1. One could try to use ray_trace_gain to emphasize the black outlines in the front. See here: http://www.pymolwiki.org:8888/index.php/Ray_trace_gain