[Chimera-users] Visualisation in Headless Chimera

Greg Couch gregc at cgl.ucsf.edu
Wed Apr 3 18:07:11 PDT 2019

You have Chimera 1.13.1, not ChimeraX.  ChimeraX is our eventual 
replacement for Chimera and "early releases" are available from 
https://www.cgl.ucsf.edu/chimerax/.  ChimeraX's scripting is similar to 
Chimera, and the graphics are much better.

     -- Greg

On 4/3/2019 12:51 AM, James Starlight wrote:
> 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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