From: John Stone (
Date: Thu Apr 22 2010 - 17:22:33 CDT

  Any time you get a different result from the Acrobat 3-D capture
than you see on the screen in VMD, it is due to a bug in the Acrobat
capture program. They intercept (literally!) all of the VMD OpenGL
commands and convert them into their own internal geometry/material

All that being said, I would try the following:
  Instead of using Licorice, try using VDW + Bonds and see if that
produces any different result or not.

If you get a different result, then this will be something for
me to fiddle with. If not, then the next thing to try is just to
display the atoms with VDW and see if you get the right coloring
there or not.

Let me know what those experiments produce for you and I should
be able to give you some further suggestions to work around the
limitations of the Adobe capture program.


On Thu, Apr 22, 2010 at 03:56:52PM -0400, Bob Johnson wrote:
> Hello everyone,
> I am using VMD and Adobe Acrobat to create a 3D PDF (or better yet...a
> u3d file that I can embed in a Power Point). However, I'm experiencing
> a problem when using the Licorice representation. When I capture the
> VMD scene with Acrobat, the color of the spherical endcaps do not
> match that of the bonds. It seems that the spheres take on the color
> of the very first bond and are not changed for the rest of the
> molecule. Here is an image as an example:
> As you can see, the spheres are red which matches the color of the
> very first residue in the protein. However, the color of the sphere is
> not updated to match the remaining residues.
> I was able to fix this when importing the object in the PRC
> Tessellation format. However, this is undesirable since I eventually
> want to embed the object in a Power Point as a .u3d file. It seems
> that the U3D import format colors all these spheres the same way. How
> can I fix this?
> Thanks,
> Bob
> --
> Bob Johnson, PhD
> Institute for Computational Molecular Science
> Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122

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