From: Eric Smoll (ericsmoll_at_gmail.com)
Date: Thu Oct 16 2014 - 14:07:32 CDT

Hello John,

Thank you for the suggestion:

OpenGL: White background with black cylinders visible
Povray rendered png: White background only. No cylinders visible.

Best,
Eric

On Thu, Oct 16, 2014 at 1:00 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Try hiding the molecule and render only your cylinders and see if they
> show up or not, and make sure they are different color than the
> background...
>
> Cheers,
> John
>
> On Thu, Oct 16, 2014 at 12:53:04PM -0600, Eric Smoll wrote:
> > On Thu, Oct 16, 2014 at 12:19 PM, John Stone <[1]johns_at_ks.uiuc.edu>
> wrote:
> >
> > Eric,
> > A 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?A (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 (DebianA
> > (x86_64-linux-gnu-g++ 4.3.3 @ x86_64-pc-linux-gnu))
> > A
> >
> > 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,
> > A John Stone
> > A [2]vmd_at_ks.uiuc.edu
> > On Thu, Oct 16, 2014 at 12:01:57PM -0600, Eric Smoll wrote:
> > >A A Hello John,
> > >
> > >A A Unfortunately, large black filled cylinders also refuse to
> show
> > up with
> > >A A povray. My issueAA goes beyond infinitesimal width of a
> line.
> > >A A Interesting, when I visualize the bounds of my system with
> thick
> > blue
> > >A A "lines" (perhaps they are cylinders) drawn with "pbc box",
> povray
> > has no
> > >A A problem rendering this.
> > >
> > >A A Notes on the commands I am using:
> > >
> > >A A I set the color with "graphics top color 16". This shows up
> as
> > black in my
> > >A A opengl window.
> > >
> > >A A I draw each cylinder with "graphics top cylinder {# # #} {#
> # #}
> > radius
> > >A A 0.5 filled yes resolution 100"
> > >
> > >A A I render the image with "render POV3 name.pov povray +W# +H#
> > -Itest.pov
> > >A A -Otest.png +D +X +A +FN"
> > >
> > >A A Also note that I set the color and draw the cylinders by
> calling
> > a tcl
> > >A A function.
> > >A A Best,
> > >A A Eric
> > >A A On Wed, Oct 15, 2014 at 9:25 PM, Eric Smoll
> > <[1][3]ericsmoll_at_gmail.com>
> > >A A wrote:
> > >
> > >A A A Hello John,
> > >
> > >A A A That makes sense. Thank you for the explanation.
> > >
> > >A A A Best,
> > >A A A Eric
> > >A A A On Wed, Oct 15, 2014 at 9:03 PM, John Stone
> > <[2][4]johns_at_ks.uiuc.edu>
> > >A A A wrote:
> > >
> > >A A A A Hi,
> > >A A A A AA Ray tracers don't like lines or points, because
> they
> > are
> > >A A A A infinitesimal objects that don't have a width, and
> such an
> > >A A A A object can't ever be hit by a ray...AA VMD tries to
> > emulate
> > >A A A A lines and points by drawing very thin cylinders and
> > spheres,
> > >A A A A but there's a limit to the efficacy of this approach,
> and
> > in
> > >A A A A general it is best to draw cylinders and spheres rather
> > than
> > >A A A A lines and points when working with ray tracers...AA
> Lines
> > and
> > >A A A A points are really only useful in the context of
> > rasterization
> > >A A A A where they bear some relationship to the pixel grid of
> the
> > >A A A A screen...
> > >
> > >A A A A Cheers,
> > >A A A A AA John Stone
> > >A A A A AA [3][5]vmd_at_ks.uiuc.edu
> > >A A A A On Wed, Oct 15, 2014 at 08:46:05PM -0600, Eric Smoll
> wrote:
> > >A A A A >AA AA Hello VMD users,
> > >A A A A >
> > >A A A A >AA AA Lines generated with "graphics top line {# #
> #} {#
> > # #} width
> > >A A A A 2" show up
> > >A A A A >AA AA in theAAA OpenGL display but are not rendered
> > with a command
> > >A A A A like "render
> > >A A A A >AA AA POV3 name.pov povray +W# +H# -Iname.pov
> -Oname.png
> > +D +X +A
> > >A A A A +FN" Is there
> > >A A A A >AA AA some reason why this would fail?
> > >A A A A >AA AA Best,
> > >A A A A >AA AA Eric
> > >
> > >A A A A --
> > >A A A A NIH Center for Macromolecular Modeling and
> Bioinformatics
> > >A A A A Beckman Institute for Advanced Science and Technology
> > >A A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL
> > 61801
> > >A A A A [4][6]http://www.ks.uiuc.edu/~johns/AA AA AA AA
> AA A
> > Phone:
> > >A A A A [5]217-244-3349
> > >A A A A [6][7]http://www.ks.uiuc.edu/Research/vmd/
> > >
> > > References
> > >
> > >A A Visible links
> > >A A 1. mailto:[8]ericsmoll_at_gmail.com
> > >A A 2. mailto:[9]johns_at_ks.uiuc.edu
> > >A A 3. mailto:[10]vmd_at_ks.uiuc.edu
> > >A A 4. [11]http://www.ks.uiuc.edu/~johns/
> > >A A 5. tel:[12]217-244-3349
> > >A A 6. [13]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
> > [14]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> > [15]217-244-3349
> > [16]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > Visible links
> > 1. mailto:johns_at_ks.uiuc.edu
> > 2. mailto:vmd_at_ks.uiuc.edu
> > 3. mailto:ericsmoll_at_gmail.com
> > 4. mailto:johns_at_ks.uiuc.edu
> > 5. mailto:vmd_at_ks.uiuc.edu
> > 6. http://www.ks.uiuc.edu/~johns/A
> > 7. http://www.ks.uiuc.edu/Research/vmd/
> > 8. mailto:ericsmoll_at_gmail.com
> > 9. mailto:johns_at_ks.uiuc.edu
> > 10. mailto:vmd_at_ks.uiuc.edu
> > 11. http://www.ks.uiuc.edu/~johns/
> > 12. tel:217-244-3349
> > 13. http://www.ks.uiuc.edu/Research/vmd/
> > 14. http://www.ks.uiuc.edu/~johns/
> > 15. tel:217-244-3349
> > 16. 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/
>