## VMD-L Mailing List

**From:** John Stone (*johns_at_ks.uiuc.edu*)

**Date:** Thu Oct 16 2014 - 14:11:34 CDT

**Next message:**Eric Smoll: "Re: "graphics top line" and "render POV3""**Previous message:**John Stone: "Re: "graphics top line" and "render POV3""**In reply to:**Eric Smoll: "Re: "graphics top line" and "render POV3""**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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/

**Next message:**Eric Smoll: "Re: "graphics top line" and "render POV3""**Previous message:**John Stone: "Re: "graphics top line" and "render POV3""**In reply to:**Eric Smoll: "Re: "graphics top line" and "render POV3""**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]