VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 15:42:08 CDT

Hi,
  The issue is that the POV-Ray scene file format is an ASCII format,
and the floating point coordinates for the rendered geometry either lacks
sufficient precision, or contains excessive precision causing the scene
file size to be bloated to hundreds of megabytes, depending on the scenario.
I would suggest trying VMD 1.8.6, as we have made a number of improvements
to the precision of the coordinates sent to POV-Ray in that version of VMD,
which may cure your problem. If not, then we can work through the details
of what you're rendering. If I can reproduce the problem here, I can
write filters to prevent such geometry from being written to the scene
file, though this will result in missing or "invisible" geometry when
the final scene is rendered. Let me know if you have a reproducable
test case that still occurs with VMD 1.8.6.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 10, 2007 at 06:22:37PM -0400, Robin L Hayes wrote:
> Hello,
>
> I am having the same problem as Amadeu on May 05, 2006. Namely, I am attempting to use vmd 1.8.5 combined with POV-Ray 3.6.1c on Windows to generate a movie of a CPMD trajectory of a molecular crystal. When I omit HBonds, each frame renders correctly. However, when I include HBonds, about 25% of the frames generate the following error in POV-Ray:
>
> Parse Error: Degenerate cylinder, base point = apex point.
>
> I can switch which frames have the problem by resetting the view and re-applying the transformations (rotate y by 90, rotate z by 90, scale by 1.75), but I can't eliminate the problem entirely. Presumably, the former changes which numbers are small. The previous thread gave the solution, "apply transformation matrix tricks to the exported geometry so POV-Ray doesn't have problems with very small numbers". It's unclear to me which tricks I should apply or whether it is possible to apply those tricks before the POV-Ray files are written. Thanks.
>
> Robin 

-- 
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