From: Michael K. Gilson (gilson_at_umbi.umd.edu)
Date: Mon Aug 31 2009 - 16:22:55 CDT

Hi John,

Yes, cylinders and lines work! I'll see what I can do with these.
Please let me know if/when you get the cones working. I think they make
the best display for my purposes, since they won't get confused with bonds.

Thanks very much!

Sincerely,
Mike

John Stone wrote:
> 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
>>
>
>

-- 
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