From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 13 2010 - 12:42:33 CDT

Hi,
  You said that when you render with Tachyon you got the default colors.
Did you see the expected coloring in the VMD OpenGL window, and not in
Tachyon, or you never got the colors that you were expecting? Which
version of VMD are you running, and how did you load the structure
file(s)? Do you load the files from the command line, text interface,
or scripting, or are you loading them from the GUI? I'm just trying to
determine whether you're causing the files to be loaded prior to your
vmd.rc file being parsed, etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 10, 2010 at 03:37:23PM -0400, Fatemesadat Emami wrote:
> Dear vmd users,
> I want to load some peptides into vmd in a way that each amino acid has
> its own color. To do that I added "mol default color resname" to .vmd.rc
> file. Now how can I define the colors for each amino acid (e.g. I want lys
> to be red, arg to be tan etc, or res1 to be red, res2 to be tan and ...).
> I mean I want to change the color sequence asign to amino acids in the
> molecule.
>
> acually I could do that (e.g. for LYS) by"
> mol color colorID 5
> mol selection {resname ARG}
> mol addrep top
> mol color colorID 1
> mol selection {resname LYS}
> mol addrep top
> mol color colorID 3
> mol selection {resname LEU}
> mol addrep top
> mol color colorID 11
> mol selection {resname PRO}
> mol addrep top
> and ...
>
> BUT when I render the image by Tachyon, it shows the default colors!!! as
> if I haven't done anythig.
>
> I wonder if somebody can help me on that.
> Thank you very much
> Fatima
>
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
> The University of Akron

-- 
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