From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 31 2009 - 14:50:33 CDT

Michael,
  Thanks for double-checking. If Adobe's Acrobat3D OpenGL capture isn't
getting cones right, then I'll have to write special code for that case.
If you change your script to draw cylinders rather than
cones, does Acrobat3D capture them correctly?
If so, then I suspect the Acrobat3D capture utility isn't handling triangle
fans correctly, and I'll have to dig into our rendering code a bit to work
around this bug in their capture utility. We already do a bunch of
special-case rendering code paths to support Acrobat3D, so this would
just be one more. This one is a bit invasive compared to others so it may
be a while before I can provide you with a modified VMD version to test.
Can you get by with drawing cylinders, lines, or something else rather than
cones for your PDFs in the mean time?

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Mon, Aug 31, 2009 at 03:36:49PM -0400, Michael K. Gilson wrote:
> Hi John,
>
> Thanks very much for looking at this. I do get this result with
> Display--> Rendermode set to Acrobat3D. I just double-checked.
>
> Best regards,
> Mike
>
> John Stone wrote:
>
> Michael,
> Interesting. The VMD renderer has a special code path it uses when
> drawing for Acrobat. Did you make sure to set the Display->Rendermode
> to "Acrobat3D" when generating this scene? If not, then please do so
> and try again. If you already had it set, then it seems that
> Acrobat's OpenGL capture has a few more limitations I hadn't
> already written workarounds for, and I'll have to write code to
> special-case the cone drawing too. Let me know which mode you were in
> when you did the OpenGL capture, and we'll go from there.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Aug 31, 2009 at 07:24:06AM -0400, Michael K. Gilson wrote:
>
>
> Hi,
>
> I am using Acrobat 9.0 Pro Extended to generate 3D PDFs from VMD. The
> molecules look okay, but my draw objects do not. It's not just a
> rendering problem: the coordinates are not correct. You can view the
> problem and the file that creates the draw objects here:
> http://gilsonlab.umbi.umd.edu/supp-mat1a.html. (Scroll down to the
> header "3D PDF problem with VMD draw objects".
> I'd appreciate guidance and/or bug-fixes!
>
> Best regards,
> Mike
>
> P.S. Sorry if this query appears twice. My first attempt has been
> pending for a few days, so I thought I'd better try again with out
> attachments.
>
>
>
>
> --
> Michael K. Gilson, M.D., Ph.D.
> CARB Fellow and Professor
> Center for Advanced Research in Biotechnology
> University of Maryland Biotechnology Institute
> 9600 Gudelsky Drive
> Rockville, MD 20850
> Voice: 240-314-6217
> Fax: 240-314-6255
> gilson<at>umbi.umd.edu
> Lab Page: gilsonlab.umbi.umd.edu
> BindingDB: www.bindingdb.org

-- 
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