VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 25 2004 - 14:01:21 CDT

Luis,
  I don't know if you're aware, but we completely rewrote the POV-Ray
surface export code for the next version of VMD. If you've got a few
minutes to try it out, have a look and tell us what you think:
  http://www.ks.uiuc.edu/Research/vmd/alpha/
 
Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 25, 2004 at 01:47:59PM -0500, Luis Rosales wrote:
> 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
> > --------------------------------------------------------------
> > ----------
> >
> >
> >
>
> 

-- 
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