VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 17 2010 - 16:07:16 CST

Hi,
  You can set all of the VMD transformation, rotation, scaling,
and centering matrices to identity matrices, which should cause the emitted
POV-Ray scene to be written in molecule coordinates. It will not look right
on the VMD display when you do this (since that messes up all of the transforms
for OpenGL), but it should emit the kind of POV-Ray geometry that you're
after. Conversely, you can use a VMD script to transform any molecule
coordinates you want into the world or eye coordinates used by POV-Ray,
Tachyon other renderers. I just sent a script for this kind of thing
to the mailing list last week. Either way, it should be possible to get
what you need.

Cheers,
  John

On Wed, Feb 17, 2010 at 01:56:34PM -0800, gschlau-cohen_at_berkeley.edu wrote:
> Thanks for the information. I have the "plot.pov" file but the problem I
> have now is that the povray coordinates are not the coordinates in the
> molecular frame from the pdb file. Can I generate a povray file in the
> same coordinates or is there a way to transform the molecular coordinates
> into the povray frame?
>
> Thanks,
> Gabriela
>
> >
> > Hi,
> > VMD should have generated the "plot.pov" for you, the error you're
> > getting is because VMD was trying to subsequently launch POV-Ray on
> > the scene file it generated, but it couldn't find the 'povray'
> > executable, so that second stage didn't complete. You can of course
> > use the plot.pov file that VMD generated and feed it into your megapov
> > install yourself.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Feb 17, 2010 at 08:44:02AM -0800, gschlau-cohen_at_berkeley.edu
> > wrote:
> >> I just downloaded VMD and am trying to create a file that I can load
> >> into
> >> povray to add other objects onto within povray. When I run:
> >> povray +W512 +H512 -Iplot.pov -Oplot.pov.tga +D +X +A +FT
> >> I get this error:
> >> povray: command not found.
> >>
> >> I have povray on my computer, but am running it through megapov.
> >>
> >> Does anyone know how to get a povray input out of vmd?
> >>
> >> Thanks,
> >> Gabriela
> >
> > --
> > 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
> >
>
>
> --
> Gabriela S. Schlau-Cohen
> PhD Candidate, Department of Chemistry
> University of California, Berkeley
>
> B77 Hildebrand Hall
> UC Berkeley Chemistry Department
> Berkeley, CA 94720
> Tel: 510-643-7609 

-- 
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