VMD-L Mailing List

From: Bob Johnson (bobjohnson1981_at_gmail.com)
Date: Fri Apr 23 2010 - 09:59:08 CDT

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