From: Josh Vermaas (
Date: Wed Aug 06 2014 - 09:21:04 CDT

What I do is similar to what you have tried. The trick I've found is to
make the transparent representation only infinitesimally larger (3.001
vs 3 for the radius for instance), which you'll need to setup with the
tkconsole, as the gui doesn't give you the resolution you need to make
it look good. From there you usually need to play with the materials to
give the right effect (I personally think that transparent uses too much
ambient lighting, but thats personal preference). Keep in mind that you
can play with your shaders (Display->Rendermode->GLSL) so that
transparent doesn't look hideous in the OpenGL window too to make
manipulating the materials easier to judge.
-Josh Vermaas

On 8/6/14, 2:49 AM, Tristan Croll wrote:
> I'm trying to find the best way to visualise residues by some property
> (e.g. conservation, favourability score on the Ramachandran plot,
> charge ...) while still keeping standard CPK colouring to make the
> residue types easy to recognise. Just wondering, how hard would it be
> to add a visualisation that makes the atoms "glow" with a colour set
> by the beta or occupancy column? The effect I'm thinking of is rather
> like the image on the front page of I can get a reasonable
> effect by using a licorice representation in CPK, and overlaying that
> with a thicker but transparent representation with my desired
> colouring, but transparent licorice doesn't render at all well.
> Cheers,
> Tristan