From: Willie Maddox (
Date: Tue Mar 30 2010 - 14:17:33 CDT


I am trying to find a software package that will allow me to manipulate the
colouring of bonds between atoms based on the bond length.

For example, if the ideal bond length in a particular crystal is say 2.0
angstroms and I perform a slab relaxation, I would like to display the bonds
that got stretched with one colour (say blue), and the bonds that got
compressed, with another (red maybe).

In addition, I would like to be able to map the range of bond lengths in
this relaxed crystal to the red/blue colour gradient, or any other colour
gradient for that matter. In other words, a bond length of 2.2 Angstroms
would appear "more" blue than a neighbouring bond 2.1 Angstroms long. Vice
versa for the reds of course.

Question: Does VMD have this ability, or can VMD be programmed to do this?

Thanks in advance!

-Willie Maddox