VMD-L Mailing List

From: Amadeu (akwsum_at_gmail.com)
Date: Fri May 05 2006 - 09:48:43 CDT

Hi John,

Thanks for your quick reply.

Yes, I do get this error message every time I try to render HBonds. I
tried the simplest case of few water molecules to a large structure
with lots of water molecules.

I am using the latest stable version of POV-Ray 3.6 for Windows.

Thanks for the help.

         --Amadeu

On 5/5/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
>