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