VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Aug 06 2014 - 01:49:00 CDT

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 fold.it... 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