Tag Archives: PyMOL

Making small molecules look good in PyMOL

Another largely plagiarized post for my “personal notes” (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules.  For my slowly-progressing confirmation report I needed some beautiful small molecule representation.  Here is some PyMOL code:

show sticks
set ray_opaque_background, off
set stick_radius, 0.1
show spheres
set sphere_scale, 0.15, all
set sphere_scale, 0.12, elem H
color gray40, elem C
set sphere_quality, 30
set stick_quality, 30
set sphere_transparency, 0.0
set stick_transparency, 0.0
set ray_shadow, off
set orthoscopic, 1
set antialias, 2
ray 1024,768

And the result:

ligand

Beautiful, no?

Good looking proteins for your publication(s)

Just came across a wonderful PyMOL gallery while creating some images for my (long overdue) confirmation report.  A fantastic resource to draw sexy proteins – especially useful for posters, talks and papers (unless you are paying extra for coloured figures!).

It would be great if we had our own OPIG “pymol gallery”.

An example of one of my proteins (1tgm) with aspirin bound to it:

Good looking protein