VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 11 2004 - 10:57:55 CST

Hi,
  This is somewhat tricky, as the method depends on whether you're
using a version of the XYZ plugin that converts the periodic element
numbers into atom name strings or not. Assuming you are (the newest
versions do), then you can specify a "name" atom selections and
draw the specifically colored atoms with with their own representations,
which works with any version of VMD. If you're using an old XYZ plugin,
the "names" might actually be the integer element numbers.

If you don't want to manually set the color but rather want the specific
atoms to get a specific color by default, you can set them in the color
window (Main->Graphics->Colors). Highlight "Name", then the atom name
of interest, then the color you want to assign it.

If that still isn't what you're looking for, let me know.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 08, 2004 at 06:06:34PM +0900, Akiyama, Jotaro wrote:
> Hi all VMD users.
>
> I have trouble in coloring atoms.
> I have two atom types which are named by integer as .xyz formal file.
> Can I color the each atom type by number?
>
> The format is as below.
> (Assuming two atoms of atom type 1 and two atoms of atom type 2
> and I would like to color type 1 red and type 2 blue.)
>
> atom type number x y z
> for example
> 1 x y z
> 1 x y z
> 2 x y z
> 2 x y z
>
>
> For sure, I use windows version on windows 2000.
>
>
> Thanks.
>
> Akiyama 

-- 
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