VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 20 2007 - 12:53:21 CST

Julien,
  I've reproduced your problem, and it is as I suspected, the isosurface
is ill-defined at an isovalue of zero. The isosurface extraction
code in VMD includes a safety check that prevents it from drawing triangles
where the interpolated vertex coordinate is calculated under conditions
leading to numerical instability. If I disable the safety checks
your surface will render without the holes, but other ill-defined datasets
could render badly or cause a runtime floating point exception due to
division by a value that's nearly zero. If you like I would be happy to
provide you with a binary that disables the safety check for the time being,
so that you can make your figures, while I see if I can implement the safety
check just slightly differently to allow you to get your surface even though
this specific case is definitely marginal at best. Try rendering the
isosurface for isovalues 0, 0.0001, and 0.000001 and you'll see how
small the volume gradient is at the outer edges of your box.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 20, 2007 at 06:24:16PM +0100, Avell Diroll wrote:
> Hi John,
>
> I am using VMD-1.8.5 on two workstations, and the same behaviour his
> observed ... but both use nvidia video card :
>
> *32bits system / VMD-1.8.5 32b / GeForce 6200 / nvidia bin driver 8776
> *64bits system / VMD-1.8.5 64b / Quadro FX 1300 / nvidia bin driver 8776
>
> I will test this dataset on some other hardware tomorrow.
>
> Once gzipped the .dx file is roughly 2 MB so it should be accepted
> through e-mail but I think that sending attachment to VMD-L is not the
> best thing to do, so sorry for not posting to the list.
>
> Thanks,
>
> Julien Lefeuvre
> 

-- 
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