From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 24 2012 - 10:32:08 CDT

Fred,
  The STL loading feature of VMD imports the triangle mesh as a VMD
graphics object, similar to what happens if you use the VMD "draw"
commands. The imported triangle mesh can't be edited or manipulated in
any meaningful way and it doesn't interact with the molecular representations
since it is non-atomic information. The STL format is a particularly
poor file format in terms of lack of information about color, material
properties, etc, so it really exacerbates the situation with VMD since
VMD expects this information to be set when the graphics geometry is loaded.

I am planning on revising how some of this functionality works in VMD
to better support some science applications that need to work with
a multiplicity of triangle meshes which are somewhat more closely
coupled with the molecular structure (e.g. vertices are tagged/associated
with atoms/particles in a simulation etc).

In the mean time, you could write a script to load your triangle mesh
into VMD using draw commands and that would allow you to directly control
the colors and material properties for the mesh.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 23, 2012 at 12:05:46PM -0400, Phelan Jr, Frederick R. Dr. wrote:
> We have a simulation that uses very definitive and structured boundaries
> at the top and bottom of the simulation box. We have created a
> representation of the lower boundary in STL and imported into VMD using
> "File>New Molecule...", and the structure does display correctly. The
> problem is that we don't seem to be able to change the color or
> manipulated the features of the structure in any way ... have tried
> everything under "Representation...", but there are no displayable
> entities that show up to manipulate.
>
>
>
> Is the problem the way we have loaded the structure, or is there just no
> way to manage the color/lighting of such an entity? Is there another way
> to load such a background feature?
>
>
>
> Thanks,
>
> Fred
>
>
>
>
>
>
>
>
>
> --------------------------------------------------------------------------
>
> Frederick R. Phelan Jr., Ph.D.
> Complex Fluids Group
> Polymers Division
> National Institute of Standards and Technology
>
> --------------------------------------------------------------------------
>
> NIST, Bldg. 224/Rm. A209
> 100 Bureau Dr., STOP 8542
> Gaithersburg, MD 20899-8542
> 301.975.6761 (VOX)
> 301.975.4924 (FAX)
> frederick.phelan_at_nist.gov
>
> My Polymers Home Page
>
>
>
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078