VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 18 2009 - 10:59:37 CDT

Nicolas,
  Yes, you should be able to use the new "outline" material properties
(and several example materials) to get edge outlines, both in VMD itself,
and with Tachyon, as described here (make sure to enable the GLSL rendering
mode to try it in VMD itself):
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/glsloutline/

If this isn't what you had in mind, send me an example image that
shows me what you're doing and why it's different than the technique
we've got built-in in VMD 1.8.7 and I'll see if I have an alternative
suggestion. My hunch is that you'll be able to get what you want by
tweaking the material properties in VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 18, 2009 at 05:54:44PM +0200, Nicolas Sapay wrote:
> Thanks for the quick answer,
>
> I send you the files off the list. The problem is that I wanted to use
> POV-Ray to add an extra effect on the picture, i.e. outlining the shape
> of the structure by a thin black line. Is it possible to do that with
> Tachyon or TachyonInternal?
>
> Cheers,
> Nicolas
>
> John Stone a écrit :
> >Nicolas,
> > Hmm, I hadn't encountered that before, I'll have to look at the
> >POV-Ray export code. The "nan" looks to me like we've got a degenerate
> >triangle getting exported, which is definitely undesirable. I would
> >suggest
> >that you try rendering the same scene using TachyonInternal, which will
> >avoid
> >the file generation step, and thus avoid the problem with the NaN numeric
> >value
> >being emitted and then later failing to parse. Try that and let me know if
> >it works for you. Ultimately, I'll probably have to add a bit of code that
> >catches this situation. Can you send me a tar.gz file containing the
> >structure
> >and VMD saved state that results in the scene that triggers the problem?
> >If you can send it to me, I should be able to reproduce it here and change
> >the
> >code to prevent this from occuring.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Aug 18, 2009 at 04:53:10PM +0200, Nicolas SAPAY wrote:
> >
> >>Hello,
> >>
> >>I'm trying to render a picture with POV-Ray using a pov file generated by
> >>VMD. Unfortunately, POV-Ray crashes at the following line:
> >>
> >>// MoleculeID: 0 ReprID: 4 Beginning polyhedra
> >>VMD_triangle(<-0.28497034,0.30557495,2.2290211>,<-0.28497034,0.30557495,2.229021
> >>1>,<-0.28497034,0.30557495,2.2290211>,<nan
> >>Parse Error: Expected 'numeric expression', undeclared identifier 'nan'
> >>found
> >> instead
> >>
> >>The problem comes from the polyhedra representation used on some part of
> >>my system. From what I understand about the VMD_triangle macro, it looks
> >>like a corner of the polyhedra is missing in the pov file. Does someone
> >>have ever faced this problem?
> >>
> >>Cheers,
> >>Nicolas
> >>
> >>--
> >>[ Nicolas Sapay - Post-Doctoral Fellow ]
> >>CERMAV - www.cermav.cnrs.fr
> >>BP53, 38041 Grenoble cedex 9, France
> >>Phone: +33 (0)4 76 03 76 44/53
> >>
> >
> > 

-- 
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