From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 23 2010 - 12:54:49 CDT

Bob,
  Thanks for the details. It sounds to me like the Adobe capture utility
has a bug that affects OpenGL display lists. From the sound of it, they
are not correctly tracking the active color and are instead using the
color state that was active at the time the display list was created.
I can probably fix this, but it will slow down rendering for the Acrobat3D
capture mode quite substantially. The workaround will be to disable the
use of the sphere display lists and see if that cures the problem or not.
I'll see if I can get this done next week.

Cheers,
  John

On Fri, Apr 23, 2010 at 10:59:08AM -0400, Bob Johnson wrote:
> The same thing happened with VDW + Bonds. It seems that the spheres
> can only be displayed as a single color when imported in this U3D
> format.
>
> I'll let you know if I find anything else. However, for now I'll just
> use the Bonds representation.
> Thanks,
> Bob
>
> On Thu, Apr 22, 2010 at 6:22 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Bob,
> >  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
> > format.
> >
> > 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.
> >
> > Cheers,
> >  John
> >
> > 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:
> >> http://astro.temple.edu/~rjohnson/temp/capture.png
> >>
> >> 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
> >> http://astro.temple.edu/~rjohnson
> >
> > --
> > 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
> >
>
>
>
> --
> Bob Johnson, PhD
> Institute for Computational Molecular Science
> Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> http://astro.temple.edu/~rjohnson

-- 
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