From: Eric Smoll (ericsmoll_at_gmail.com)
Date: Thu Oct 16 2014 - 13:53:04 CDT

On Thu, Oct 16, 2014 at 12:19 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Eric,
> Did you have a look at the .pov file generated by VMD?
> I assume that your cylinders are there, yes?
>

Correct. They are in the file. I checked this.

>
> Does POV-Ray print any warnings about deleting degenerate objects or
> anything else? (POV-Ray will sometimes delete or exclude geometry
> that it thinks is too small to be visible)
>
> No. No error beyond a warning that I do not have a povray config file
setup ("povray: cannot open the user configuration file"). I believe this
is optional. Here is my version information:
Persistence of Vision(tm) Ray Tracer Version 3.6.1 (Debian
(x86_64-linux-gnu-g++ 4.3.3 @ x86_64-pc-linux-gnu))

> Do you have this problem is the VMD scene is empty other than
> your cylinder, or only when you've also loaded a molecule?
>

I have a large scene loaded. All the molecules are rendered perfectly. Only
the cylinders are omitted.

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Oct 16, 2014 at 12:01:57PM -0600, Eric Smoll wrote:
> > Hello John,
> >
> > Unfortunately, large black filled cylinders also refuse to show up
> with
> > povray. My issueA goes beyond infinitesimal width of a line.
> > Interesting, when I visualize the bounds of my system with thick blue
> > "lines" (perhaps they are cylinders) drawn with "pbc box", povray has
> no
> > problem rendering this.
> >
> > Notes on the commands I am using:
> >
> > I set the color with "graphics top color 16". This shows up as black
> in my
> > opengl window.
> >
> > I draw each cylinder with "graphics top cylinder {# # #} {# # #}
> radius
> > 0.5 filled yes resolution 100"
> >
> > I render the image with "render POV3 name.pov povray +W# +H#
> -Itest.pov
> > -Otest.png +D +X +A +FN"
> >
> > Also note that I set the color and draw the cylinders by calling a tcl
> > function.
> > Best,
> > Eric
> > On Wed, Oct 15, 2014 at 9:25 PM, Eric Smoll <[1]ericsmoll_at_gmail.com>
> > wrote:
> >
> > Hello John,
> >
> > That makes sense. Thank you for the explanation.
> >
> > Best,
> > Eric
> > On Wed, Oct 15, 2014 at 9:03 PM, John Stone <[2]johns_at_ks.uiuc.edu>
> > wrote:
> >
> > Hi,
> > A Ray tracers don't like lines or points, because they are
> > infinitesimal objects that don't have a width, and such an
> > object can't ever be hit by a ray...A VMD tries to emulate
> > lines and points by drawing very thin cylinders and spheres,
> > but there's a limit to the efficacy of this approach, and in
> > general it is best to draw cylinders and spheres rather than
> > lines and points when working with ray tracers...A Lines and
> > points are really only useful in the context of rasterization
> > where they bear some relationship to the pixel grid of the
> > screen...
> >
> > Cheers,
> > A John Stone
> > A [3]vmd_at_ks.uiuc.edu
> > On Wed, Oct 15, 2014 at 08:46:05PM -0600, Eric Smoll wrote:
> > >A A Hello VMD users,
> > >
> > >A A Lines generated with "graphics top line {# # #} {# # #}
> width
> > 2" show up
> > >A A in theAA OpenGL display but are not rendered with a
> command
> > like "render
> > >A A POV3 name.pov povray +W# +H# -Iname.pov -Oname.png +D +X +A
> > +FN" Is there
> > >A A some reason why this would fail?
> > >A A Best,
> > >A A Eric
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [4]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> > [5]217-244-3349
> > [6]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > Visible links
> > 1. mailto:ericsmoll_at_gmail.com
> > 2. mailto:johns_at_ks.uiuc.edu
> > 3. mailto:vmd_at_ks.uiuc.edu
> > 4. http://www.ks.uiuc.edu/~johns/
> > 5. tel:217-244-3349
> > 6. http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>