From: John Stone (
Date: Fri Aug 10 2007 - 15:09:49 CDT

  Please check out the various VMD tutorials that are available.
There are a number of good examples that describe various ways of
applying user-defined coloring to structures by setting the
"Beta" and "User" fields using the atom selection text commands,
depending on whether you want a static, unchanging color scheme or
a time-varying color scheme. I think Axel's CPMD-VMD tutorial in
particular shows a couple of these.

  John Stone

On Fri, Aug 10, 2007 at 03:13:42PM -0400, Naresh wrote:
> Hi all,
> Is there a way to color a protein based on a property value I
> calculate (through CHARMM) for each residue. I have both time
> averaged and instantaneous values of this property which varies from
> residue to residue along the sequence. I would like to look at this
> property on the protein structure in one of the representations (such
> as cartoon), either the averaged value or instantaneous one with
> simulation.
> Thanks,
> -Naresh

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078