VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 20 2007 - 10:44:36 CST

Hi Julien,
  What video card and driver are you using?
I haven't seen the behavior you're getting previously,
so I would definitely like to get a copy of the DX file
you're loading, and a VMD saved state file that creates
the view that you posted. My initial guess as to the cause
of this problem is that the surface normal (e.g. volume gradient)
is very close to zero at the points where the triangles start looking
weird. If so, the surface is ill-defined at those points.
Nevertheless, I may be able to to tweak differential measurement
used to calculate the volume gradient to perform better with this
dataset if you can send me a copy.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 20, 2007 at 03:52:35PM +0100, Avell Diroll wrote:
> Dear VMD-L,
>
> First I would like to thank all the VMD developers for their great work.
>
> However, I am experiencing a little problem right now ...
>
> I am using VMD (Linux) to display some isosurfaces of molecular
> lipophilic potential (loaded from an .dx file).
> Everything is fine as long as closed surfaces are displayed, but the
> interpolation of "open" surfaces (such as an isosurface associated to a
> null potential), "forgets" to show some of the triangles between grid
> points. (these are wild guesses as I did not dig the problem further)
>
> You may find a sample snapshot of the result here :
> http://img518.imageshack.us/my.php?image=snapen0.png
>
> I can provide all the files needed to reproduce this behaviour (grid
> data is 5.2 MB).
>
> I tried the different rendermode available but the problem remains in
> all modes.
> I also tested my grid data on some other visualization programs (namely
> : chimera and pymol) and the surfaces are displayed as expected on those.
>
> I did not find any references to this in the mailing list or in the
> VMD-1.8.6 development log, nor did I found a work around by myself.
>
> Please let me know if I missed something or if there is a work around
> for that.
>
> Regards,
>
> Julien Lefeuvre
>
> --
> __________________________________________________________________________
> Julien Lefeuvre, PhD Student
> Institut Européen de Chimie et de Biologie (IECB)
> CNRS UMR 5144 Molécules, Biomolécules et Objets Supramoléculaires (MoBIOS)
> 2, rue Robert Escarpit - 33607 Pessac Cedex - France
> Tél. : 33 (0)5 40 00 30 31
> Fax. : 33 (0)5 40 00 30 73
> http://www.iecb.u-bordeaux.fr
> __________________________________________________________________________ 

-- 
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