VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 06 2003 - 13:06:01 CDT

Hi,
  I'm forwarding a VMD-L note that bounced this morning (must be
subscribed to VMD-L from the same address you post from, as we filter
non-member posts to prevent spammers from using VMD-L...)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

----- Forwarded message from owner-vmd-l_at_ks.uiuc.edu -----

Date: Tue, 6 May 2003 09:47:52 -0600 (MDT)
From: Brian Thomas Foley <btf_at_lanl.gov>
Reply-To: Brian Thomas Foley <btf_at_lanl.gov>
Subject: Re: new color scale
To: rhertadi_at_bio.titech.ac.jp, vmd-l_at_ks.uiuc.edu

The ConSurf tool at:

http://consurf.tau.ac.il/index.html

Already does this very well for .PDB files and
displaying in Protein Explorer (which uses RasMol
scripts, not VMD scripting).

The ConSurf tool replaces the B-factor column in a .PDB
file with values indicating the diversity or site-specific
rate of evolution of each amino acid, based on a multiple
sequence alignment (the tool builds a phylogenetic tree from
the alignment and calculates variability of each AA based
on that tree, using the Rate4Site tool:
http://ashtoret.tau.ac.il/~rebell/)

ConSurf then uses a color mixing scheme to display the
rate variation on the 3D structure by coloring each amino
acid a different shade from blue through purple.

 ______________________________________________________________
|Brian T. Foley btf_at_t10.lanl.gov |
|HIV Genetics and Immunology Databases (505) 665-1970 |
|Los Alamos National Lab |
|Los Alamos, NM 87545 U.S.A. http://hiv-web.lanl.gov/ |
|______________________________________________________________|

> I would like to make a new color scale by VMD for coloring the beta factor
> of a protein. For example I want the lowest value of B-factor is blue and
> the highest one is red and the intermediate value is the the mixture of
> these colors. Can anyone give me the sample script how to modify the color
> scale to meet with my purpose.
>
>
> Rukman

----- End forwarded message ----- 

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