From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 07 2005 - 13:17:20 CST

Paul,
  If you're reading the POV-Ray scene file, the coordinate system sent
to POV-Ray is not at all the same coordinate system specified in VMD.
We have to do various things to transform the coordinates sent to POV-Ray
so that they don't have problems when generating large surfaces etc.
If you're seeing a visible difference between the on-screen display in
VMD and in the generated POV-Ray image, then that's another matter, and
you may have found a circumstance where the coordinate system transformations
aren't doing what they should. Can you send me a very simple example
scene that illustrates the problem? (tiny molecule with VMD state,
generated POV-Ray scene file, and screen shots, and POV output image)
That should help me track down what's happening. Several people
here are using POV-Ray when rendering the "solid" clipping planes on
a regular basis, and this is the first I've heard of this problem, so
it may be unique to what you're doing. If you can provide me with test
data it'll help a lot.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 07, 2005 at 10:58:40AM -0800, Paul D. Jones wrote:
> Hi!
>
> I have noticed that if I use the clipping plane tool to clip a surface, then
> export the result to POV-ray, the exported surface is not clipped in the
> same manner as in VMD. For example, if the clipping plane is the x-y plane
> and is located at z=1 (in VMD) then in povray it will be still be the x-y
> plane, but be located at z=2, so my clipped area is off.
>
> I suppose I could manually edit the POVray script, but at 23 Mb, that would
> be quite a task :-)
>
> Any thoughts?
>
> -paul
>
>
>
> ================================
> Paul D. Jones, Ph.D.
> NIH Postdoctoral Fellow
> Department of Entomology &
> Cancer Research Center
> University of California, Davis
> Davis, CA 95616
> 530 754-8884
> ================================
>

-- 
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