VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 02 2003 - 10:33:33 CST

Hi Denys,

On Thu, Jan 02, 2003 at 02:04:10PM +0100, Denys Bashtovyy wrote:
> I'd like to know, if it is possible (and how?) in VMD to map a
> hydrophobicity (according to any scale - of Eisenberg, KD etc) on the Connolly
> surface of a protein molecule?

A common practice for this sort of thing is to set the "beta" fields
of the atoms to value you're interested in, and then color by beta, in order
to see it. Take a look at the "betacolor_distance" example in the
User's Guide, it should be very helpful in allowing you to set arbitrary
values to use in coloring surfaces:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node180.html

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078