VMD-L Mailing List

From: Luis Rosales (ludwig_at_biomedicas.unam.mx)
Date: Mon Oct 25 2004 - 13:47:59 CDT

 Hi Dominique!

In the past I used to render surfaces of earlier versions of vmd on povray,
and the "degenerate triangle" problem was a common one, however it does not
have impact on the rendering of the surfaces, as far as i know.

Personally, I dont like too much the way that vmd builds surfaces (oops,
sorry...), so I dont use it anymore to render surfaces...
Besides, Triangle meshes take looooong time to parse, so I suggest that you
try some of the following:

1. If you want to render molecular surfaces (thats protein or nucleic acid),
use GRASP and save the surface, then use pov4grasp
(http://pov4grasp.free.fr/, a modified version of povray) to render the
surface. Its faster than rendering triangle meshes and the GRASP surfaces
are smoother (and you can render properties like electrostatic potential,
curvature, etc...).

2. If you really need to render smooth triangles, triangles or meshes, you
can try the "mesh compressor" and the compressed mesh macro fro povray
(http://www.geocities.com/SiliconValley/Lakes/1434/, both from Chris
Colefax). The mesh compressor can be used to get rid of "degenerated
triangles" and by compressing the meshes, you get smaller pov files and save
a lot of time during the parsing steps of povray (and that can be important
if you are editing your pov file or making an animation).

Hope this helps,
Best Regards,

Luis

> -----Mensaje original-----
> De: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
> En nombre de Dominique Vlieghe
> Enviado el: Lunes, 25 de Octubre de 2004 07:13
> Para: vmd-l_at_ks.uiuc.edu
> Asunto: vmd-l: Problems with povray
>
> Hi,
>
> I have some problems with rendering pictures using povray. Seems that
> part of the image elements are not present in the final
> output image. I
> also get a lot of errors, being
> ...
> File: E:\dominiv\projects\integrin\structures\test.pov Line: 578
> Warning: Degenerate triangle. Please remove.
> ...
>
>
> Lines at about position 578 look like
>
> ...
> smooth_triangle {
> <-1.8559, -3.5591, 1.4187>,
> <0.5808, 0.8097, -0.0834>,
> <-1.8627, -3.5725, 1.4156>,
> <-0.5809, -0.8097, 0.0835>,
> <-1.8720, -3.5529, 1.4101>,
> <0.1325, 0.9431, -0.3050>
> texture { VMD_mat_1 }
> pigment { color rgbt <0.350,0.350,0.350,0.000> }
> no_shadow
> }
> ...
>
> this one goes wrong, although other smooth_triangle lines go well.
>
> I tested on both linux and windows (I use VMD 1.8.2 and Povray 3.5),
> but to no avail. I used VMD/povray already before, and I
> don't remember
> to have had problems then. My structures consists mainly of
> Bonds, VDW
> and NewRibbons Graphical Representations.
>
> Any clues?
>
> Regards,
>
> Dominique
>
>
>
> --
> --------------------------------------------------------------
> ----------
> Save the Hubble petition: http://www.savethehubble.org
> --------------------------------------------------------------
> ----------
> Dominique Vlieghe, Ph.D.,
> Bioinformatics Core, Department for Molecular Biomedical
> Research (DMBR)
> VIB - Ghent University
> Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium
> --------------------------------------------------------------
> ----------
> email: dominique.vlieghe_at_dmbr.ugent.be tel:
> +32-(0)9-33-13.693
> www: http://www.dmbr.ugent.be/ fax:
> +32-(0)9-33-13.609
> --------------------------------------------------------------
> ----------
>
>
>