VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 04 2002 - 15:48:37 CST

Dear Margaret, and VMD-L,
  What level of coloring granularity are you looking for?
What graphical representation do you intend to use on the residue
of interest? The existing versions of VMD allow you to create
representations and can color these representations by various properties
as I'm sure you're aware, but there are various "tricks" you can use
to get it to color by properties that aren't listed in the color by
menu. These mechanisms typically require some amount of scripting,
but it all depends, I have a few suggestions:

  - You can use the "beta" field (or many of the other fields) of atoms
    to store user specified data if you like. This data could be a true
    false value, or a scalar floating point value representating some
    attribute of interest. Once this property has been set for the
    atoms of interest, you can use the color by "beta" feature of the
    graphics menu to apply colors to your geometry. This gives you a way
    to color by properties that aren't coded into VMD already. This method
    requires that set the "beta" property of the atoms you're going to draw
    (at a minimum) using this method. The user's guide has some examples
    about this in the atomselect sections IIRC.
 
  - Another mechanism that requires less scripting would be to
    manually create a number of selections, with the coloring you like,
    using color by "colorid" in the graphics menu. Since its just one
    residue, this may be a practical option for you.

  - Yet another option is to use the "draw" commands and a little scripting
    to generate your own geometry, to make it look literally any way you
    like.

Let us know if you have more questions about this.

As always VMD-L users are encouraged to chime in with their own
suggestions...

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 02, 2002 at 06:03:45PM -0800, Margaret Cheung wrote:
>
> Dear VMD users and developers,
>
> I'd like to present one residue with different colors to highlight
> particular areas that are in contacts with other hydrophobic residues.
> Please help. Thank you very much.
>
> Sincerely,
> Margaret S. Cheung
> Biophysics Program
> Physics Department 0319
> University of California, San Diego
> 9500 Gilman Drive,
> La Jolla, CA 92093-0319
> http://www-physics.ucsd.edu/~cheung 

-- 
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              
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