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@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@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@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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