From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 16 2014 - 14:11:34 CDT

Eric,
  Please zip/gzip the .pov file for the scene where just the
black cylinders are not visible, and either send it to me by
email (don't post to VMD-L) or send me a URL where I can grab it.

Thanks,
  John

On Thu, Oct 16, 2014 at 01:07:32PM -0600, Eric Smoll wrote:
> 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 <[1]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,
> A John
>
> On Thu, Oct 16, 2014 at 12:53:04PM -0600, Eric Smoll wrote:
> >A A On Thu, Oct 16, 2014 at 12:19 PM, John Stone
> <[1][2]johns_at_ks.uiuc.edu> wrote:
> >
> >A A A Eric,
> >A A A AA Did you have a look at the .pov file generated by VMD?
> >A A A I assume that your cylinders are there, yes?
> >
> >A A Correct. They are in the file. I checked this.
> >
> >A A A Does POV-Ray print any warnings about deleting degenerate
> objects or
> >A A A anything else?AA (POV-Ray will sometimes delete or exclude
> geometry
> >A A A that it thinks is too small to be visible)
> >
> >A A No. No error beyond a warning that I do not have a povray config
> file
> >A A setup ("povray: cannot open the user configuration file"). I
> believe this
> >A A is optional. Here is my version information:
> >A A Persistence of Vision(tm) Ray Tracer Version 3.6.1 (DebianA
> >A A (x86_64-linux-gnu-g++ 4.3.3 @ x86_64-pc-linux-gnu))
> >A A A
> >
> >A A A Do you have this problem is the VMD scene is empty other than
> >A A A your cylinder, or only when you've also loaded a molecule?
> >
> >A A I have a large scene loaded. All the molecules are rendered
> perfectly.
> >A A Only the cylinders are omitted.
> >
> >A A A Cheers,
> >A A A AA John Stone
> >A A A AA [2][3]vmd_at_ks.uiuc.edu
> >A A A On Thu, Oct 16, 2014 at 12:01:57PM -0600, Eric Smoll wrote:
> >A A A >AA AA Hello John,
> >A A A >
> >A A A >AA AA Unfortunately, large black filled cylinders also
> refuse to show
> >A A A up with
> >A A A >AA AA povray. My issueAAA goes beyond infinitesimal width
> of a line.
> >A A A >AA AA Interesting, when I visualize the bounds of my system
> with thick
> >A A A blue
> >A A A >AA AA "lines" (perhaps they are cylinders) drawn with "pbc
> box", povray
> >A A A has no
> >A A A >AA AA problem rendering this.
> >A A A >
> >A A A >AA AA Notes on the commands I am using:
> >A A A >
> >A A A >AA AA I set the color with "graphics top color 16". This
> shows up as
> >A A A black in my
> >A A A >AA AA opengl window.
> >A A A >
> >A A A >AA AA I draw each cylinder with "graphics top cylinder {# #
> #} {# # #}
> >A A A radius
> >A A A >AA AA 0.5 filled yes resolution 100"
> >A A A >
> >A A A >AA AA I render the image with "render POV3 name.pov povray
> +W# +H#
> >A A A -Itest.pov
> >A A A >AA AA -Otest.png +D +X +A +FN"
> >A A A >
> >A A A >AA AA Also note that I set the color and draw the cylinders
> by calling
> >A A A a tcl
> >A A A >AA AA function.
> >A A A >AA AA Best,
> >A A A >AA AA Eric
> >A A A >AA AA On Wed, Oct 15, 2014 at 9:25 PM, Eric Smoll
> >A A A <[1][3][4]ericsmoll_at_gmail.com>
> >A A A >AA AA wrote:
> >A A A >
> >A A A >AA AA AA Hello John,
> >A A A >
> >A A A >AA AA AA That makes sense. Thank you for the explanation.
> >A A A >
> >A A A >AA AA AA Best,
> >A A A >AA AA AA Eric
> >A A A >AA AA AA On Wed, Oct 15, 2014 at 9:03 PM, John Stone
> >A A A <[2][4][5]johns_at_ks.uiuc.edu>
> >A A A >AA AA AA wrote:
> >A A A >
> >A A A >AA AA AA AA Hi,
> >A A A >AA AA AA AA AAA Ray tracers don't like lines or points,
> because they
> >A A A are
> >A A A >AA AA AA AA infinitesimal objects that don't have a
> width, and such an
> >A A A >AA AA AA AA object can't ever be hit by a ray...AAA VMD
> tries to
> >A A A emulate
> >A A A >AA AA AA AA lines and points by drawing very thin
> cylinders and
> >A A A spheres,
> >A A A >AA AA AA AA but there's a limit to the efficacy of this
> approach, and
> >A A A in
> >A A A >AA AA AA AA general it is best to draw cylinders and
> spheres rather
> >A A A than
> >A A A >AA AA AA AA lines and points when working with ray
> tracers...AAA Lines
> >A A A and
> >A A A >AA AA AA AA points are really only useful in the context
> of
> >A A A rasterization
> >A A A >AA AA AA AA where they bear some relationship to the
> pixel grid of the
> >A A A >AA AA AA AA screen...
> >A A A >
> >A A A >AA AA AA AA Cheers,
> >A A A >AA AA AA AA AAA John Stone
> >A A A >AA AA AA AA AAA [3][5][6]vmd_at_ks.uiuc.edu
> >A A A >AA AA AA AA On Wed, Oct 15, 2014 at 08:46:05PM -0600,
> Eric Smoll wrote:
> >A A A >AA AA AA AA >AAA AAA Hello VMD users,
> >A A A >AA AA AA AA >
> >A A A >AA AA AA AA >AAA AAA Lines generated with "graphics top
> line {# # #} {#
> >A A A # #} width
> >A A A >AA AA AA AA 2" show up
> >A A A >AA AA AA AA >AAA AAA in theAAAA OpenGL display but are
> not rendered
> >A A A with a command
> >A A A >AA AA AA AA like "render
> >A A A >AA AA AA AA >AAA AAA POV3 name.pov povray +W# +H#
> -Iname.pov -Oname.png
> >A A A +D +X +A
> >A A A >AA AA AA AA +FN" Is there
> >A A A >AA AA AA AA >AAA AAA some reason why this would fail?
> >A A A >AA AA AA AA >AAA AAA Best,
> >A A A >AA AA AA AA >AAA AAA Eric
> >A A A >
> >A A A >AA AA AA AA --
> >A A A >AA AA AA AA NIH Center for Macromolecular Modeling and
> Bioinformatics
> >A A A >AA AA AA AA Beckman Institute for Advanced Science and
> Technology
> >A A A >AA AA AA AA University of Illinois, 405 N. Mathews Ave,
> Urbana, IL
> >A A A 61801
> >A A A >AA AA AA AA [4][6][7]http://www.ks.uiuc.edu/~johns/AAA
> AAA AAA AAA AAA A
> >A A A Phone:
> >A A A >AA AA AA AA [5]217-244-3349
> >A A A >AA AA AA AA [6][7][8]http://www.ks.uiuc.edu/Research/vmd/
> >A A A >
> >A A A > References
> >A A A >
> >A A A >AA AA Visible links
> >A A A >AA AA 1. mailto:[8][9]ericsmoll_at_gmail.com
> >A A A >AA AA 2. mailto:[9][10]johns_at_ks.uiuc.edu
> >A A A >AA AA 3. mailto:[10][11]vmd_at_ks.uiuc.edu
> >A A A >AA AA 4. [11][12]http://www.ks.uiuc.edu/~johns/
> >A A A >AA AA 5. tel:[12]217-244-3349
> >A A A >AA AA 6. [13][13]http://www.ks.uiuc.edu/Research/vmd/
> >A A A --
> >A A A NIH Center for Macromolecular Modeling and Bioinformatics
> >A A A Beckman Institute for Advanced Science and Technology
> >A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >A A A [14][14]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA A
> Phone:
> >A A A [15]217-244-3349
> >A A A [16][15]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> >A A Visible links
> >A A 1. mailto:[16]johns_at_ks.uiuc.edu
> >A A 2. mailto:[17]vmd_at_ks.uiuc.edu
> >A A 3. mailto:[18]ericsmoll_at_gmail.com
> >A A 4. mailto:[19]johns_at_ks.uiuc.edu
> >A A 5. mailto:[20]vmd_at_ks.uiuc.edu
> >A A 6. [21]http://www.ks.uiuc.edu/~johns/A
> >A A 7. [22]http://www.ks.uiuc.edu/Research/vmd/
> >A A 8. mailto:[23]ericsmoll_at_gmail.com
> >A A 9. mailto:[24]johns_at_ks.uiuc.edu
> >A A 10. mailto:[25]vmd_at_ks.uiuc.edu
> >A A 11. [26]http://www.ks.uiuc.edu/~johns/
> >A A 12. tel:[27]217-244-3349
> >A A 13. [28]http://www.ks.uiuc.edu/Research/vmd/
> >A A 14. [29]http://www.ks.uiuc.edu/~johns/
> >A A 15. tel:[30]217-244-3349
> >A A 16. [31]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
> [32]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> [33]217-244-3349
> [34]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:ericsmoll_at_gmail.com
> 5. mailto:johns_at_ks.uiuc.edu
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. http://www.ks.uiuc.edu/~johns/AA
> 8. http://www.ks.uiuc.edu/Research/vmd/
> 9. mailto:ericsmoll_at_gmail.com
> 10. mailto:johns_at_ks.uiuc.edu
> 11. mailto:vmd_at_ks.uiuc.edu
> 12. http://www.ks.uiuc.edu/~johns/
> 13. http://www.ks.uiuc.edu/Research/vmd/
> 14. http://www.ks.uiuc.edu/~johns/A
> 15. http://www.ks.uiuc.edu/Research/vmd/
> 16. mailto:johns_at_ks.uiuc.edu
> 17. mailto:vmd_at_ks.uiuc.edu
> 18. mailto:ericsmoll_at_gmail.com
> 19. mailto:johns_at_ks.uiuc.edu
> 20. mailto:vmd_at_ks.uiuc.edu
> 21. http://www.ks.uiuc.edu/~johns/A
> 22. http://www.ks.uiuc.edu/Research/vmd/
> 23. mailto:ericsmoll_at_gmail.com
> 24. mailto:johns_at_ks.uiuc.edu
> 25. mailto:vmd_at_ks.uiuc.edu
> 26. http://www.ks.uiuc.edu/~johns/
> 27. tel:217-244-3349
> 28. http://www.ks.uiuc.edu/Research/vmd/
> 29. http://www.ks.uiuc.edu/~johns/
> 30. tel:217-244-3349
> 31. http://www.ks.uiuc.edu/Research/vmd/
> 32. http://www.ks.uiuc.edu/~johns/
> 33. tel:217-244-3349
> 34. 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/