VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 05 2006 - 09:38:02 CDT

Hi,
  Do you get this error message in all cases when you render HBonds,
or does it only happen some of the time? It could be the result of limited
precision floating point in the POV-Ray ASCII scene files that VMD generates.
I've had to work around such problems in the past by applying transformation
matrix tricks to the exported geometry so POV-Ray doesn't have problems with
very small numbers. Which version of POV-Ray are you running?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 05, 2006 at 08:09:51AM -0400, Amadeu wrote:
> I am trying to use povray to render a structure saved from VMD 1.8.4
> and I keep getting the error:
>
> Parse error: degenerate cylinder, base point = apex point.
>
> The structure I am trying to render contains hydrogen bonds (HBonds
> representation in VMD). I narrowed down that the problem is with the
> rendering of the HBonds. If I try any other representation besides
> HBonds, it works fine. I tried this with a very simple case for a
> collection of water molecules.
>
> Does anyone have any idea about this problem and possibly of a solution?
>
> Thank for the assistance.
>
> --Amadeu 

-- 
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