[Chimera-users] Visualisation in Headless Chimera

[James Starlight]

Thanks Greg!
So I need to update libOSMesa.so in the /lib of my chimera-headles, needn't it?
Actually I have found only libOSMesa.so in the lib of chimera-headless
but not in the ChimeraX - I have version 1.13.1 installed in parallel
on my ubuntu machine...

вт, 2 апр. 2019 г. в 18:20, Greg Couch <gregc at cgl.ucsf.edu>:
>
> The crash due to "set silhouette" is probably due to the ancient version
> of libOSMesa.so that is bundled with Chimera.  See my earlier response
> to you, that I mistakenly only sent to the mailing list:
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-March/015584.html.
>
> And if you're going to use povray for the final image, then "set
> silhouette" doesn't help you, as that setting is not exported, so you
> could remove it and not crash :-).
>
>      Bonne chance,
>
>      Greg
>
> On 4/2/2019 12:39 AM, James Starlight wrote:
> > Thank you very much, Elaine!
> > The only thing is to understand why "set silhouette" produces crush at
> > the stage of the image rendering both with chimera-headless or pow-ray
> > rendering ;o
> >
> > пн, 1 апр. 2019 г. в 20:10, Elaine Meng <meng at cgl.ucsf.edu>:
> >> Hi James,
> >> In my experience, i get much better images just using Chimera rendering, not POVray.  If you want shadows you can turn them on directly in Chimera (e.g. command: set shadows), and some Chimera settings are not relevant to POVray (silhouette edges, etc.).
> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
> >>
> >> However, if you really want to use it, you can set POV-Ray Options in the Preferences, save the preferences, and then copy that preferences file to the headless machine.  Still this is only a small subset of the things one could possibly change in povray, so if you’re a POVray expert you could fiddle with the POVray conf file (see Chimera Log for where this would be), and possibly re-run povray directly using the Chimera-generated .ini and .pov files (from the “copy” command with “raytrace”).
> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html>
> >>
> >> I hope this helps,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Apr 1, 2019, at 2:58 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> >>>
> >>> P.S. could you also suggest me how it would be possible to change
> >>> pov-ray options working in Headless Chimera?
> >>>
> >>> I am using it with a simple script:
> >>>
> >>> # make visualisation of b-factors
> >>> rangecolor bfactor 2 dark red 20 firebrick 40 orange red 60 orange 100 yellow
> >>>
> >>> # make a png immage
> >>> copy file ${output}/structure/${pdb_name}.png png width 800 height 600
> >>> supersample 4 raytrace rtwait" > "${temp}/chimera.${pdb_name}.com"
> >>>
> >>> As the result I have an image with the alpha channel (although I
> >>> indicated not to use it in my session via
> >>> chimera-headless ${pdb} script.com --nobgopacity
> >>>
> >>> finally I would like to change some rendeting options using the same
> >>> scripting work-flow like "Quality",  "Antialias depth"  etc
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