VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 06 2003 - 13:42:53 CST

Dear Klaus,
  I have a few suggestions for you so that you can get comparable
volumes from STL files you export from VMD:
  1) Load all of the structures you want to export at the same time.
     When exporting, toggle each of the loaded molecules on, export,
     and toggle them back off. (This lets you export them one at a time).
     There's no way to export scenes in VMD in raw non-scaled coordinates
     presently, but if people would find this useful, I could potentially
     see providing an option for doing this in a future version.

  2) I'm not sure what you have in mind regarding the color data, but
     if you want to color a 3-D solid model exported from VMD, my suggestion
     would be to use the "VRML2" export format, as this includes colors
     for all of the geometry. We have used it to create colored models with
     Z-corp 3-D printers. You can see one such model in the 4th spotlight
     item on our web page here:
       http://www.ks.uiuc.edu/Research/vmd/spotlight/

     If you want the color map used for some other purpose, you can
     query these colors via the VMD scripting interface. You can also
     override the built-in color maps as described in the User guide:
       http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node184.html

     I assume you've also seen the "betacolor_distance" example in
     the user's guide:
       http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node180.html

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 06, 2003 at 07:56:57PM +0100, Klaus Kramer wrote:
> Hi
>
> I have got two questions concerning the render section of the VMD program. My
> problem is
> that when I render different molecules that they are not in proportion to each
> other. All molecules are drawn with the SURF-Modul. When I compared the
> proportion of the molecular weights of two different molecules with the
> proportion of the rendered STL-Format volumes,
> I realized that these proprotions are different. But I need the exact
> proportion of all rendered molecules to each other. I found out that the vmd
> progam render the actual OpenGL state of the current molecule, that means a
> molecule has two different volumes, when I scale this molecule between two
> rendering actions.
> When I start the SURF program separatly from VMD with the molecule-file and
> convert the triangle list given by the SURF program in a STL-file, than I get
> the right proprotion between different molecule STL-files.
> So is there a possibility to render a molecule in VMD with the original data
> given by the SURF program?
>
> The other problem I have, is that I want to get the color data of the atoms,
> which are computed by the different coloring methods. So is there an easy way
> to write a modul, which writes these color data in a colormap ?
>
> thanks,
> klaus 

-- 
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