VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 16 2014 - 14:00:05 CDT

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/