[Chimera-users] Pov-Ray functionality

Greg Couch gregc at cgl.ucsf.edu
Mon Oct 28 16:10:37 PDT 2019

Chimera generates POV-Ray input by converting it's X3D output to POV-Ray 
with the CHIMERA/bin/x3d2pov program.  x3d2pov is tailored for Chimera's 
X3D output, but it will probably work with ChimeraX's X3D output.  To 
use it, run:

     CHIMERA/bin/x3d2pov -o FILENAME.pov < FILENAME.x3d

where CHIMERA is the location where Chimera is installed and FILENAME is 
the name of the data file.

One caveat about ChimeraX's X3D output, most X3D viewer's blindly apply 
the unit node's conversion factor to scale the coordinates, which 
results in nothing to see.  The unit node is supposed to have no effect 
in the case of a single X3D file, but in practice it does.  So to view 
the data, remove or comment out the unit node.



On 10/28/19 9:42 AM, Brown, Jeffrey wrote:
> Thank you. Will try the xcd export.
>> Cheers,
>> JWB
>> Jeffrey Wade Brown, M.D., Ph.D.
>> Instructor in Medicine
>> Washington University School of Medicine
>>  Division of Gastroenterology
>>  660 South Euclid, Campus Box 8124 <x-apple-data-detectors://4/0>
>> St. Louis, MO 63110 <x-apple-data-detectors://4/0>
>> Facsimile: (314) 362-3643 <tel:(314)%20362-3643>
>> Office: (314) 454-8204
>> Pager: (314) <tel:(314)%20407-5877>253-1585
>> E-Mail:brownjw at wustl.edu <mailto:brownjw at wustl.edu>
>> http://independent.academia.edu/JeffreyWadeBrown
> On Oct 28, 2019, at 11:39 AM, Elaine Meng <meng at cgl.ucsf.edu 
> <mailto:meng at cgl.ucsf.edu>> wrote:
>> Hello Jeffrey,
>> Ah yes, nice images!
>> ChimeraX is a different program than Chimera, being built from the 
>> ground up.  So any differences are not the result of “removal” per 
>> se, and may still be planned for future implementation. However, we 
>> do not plan for the programs to be identifical, and I don’t know of 
>> any hard decision (either way) as to whether povray export will be 
>> included.  Currently ChimeraX has directional shadows similar to the 
>> option in Chimera, and “ambient-occlusion” multishadowing, which was 
>> not available in Chimera.
>> There may be an intermediate solution:
>> In Chimera, the povray export is by making an initial X3D file and 
>> then running the x3d2pov conversion program included with Chimera (in 
>> the bin directory).
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
>> ChimeraX does have export to X3D implemented (command “save” with 
>> “format x3d”), so maybe you could do that and then “manually” run the 
>> conversion program mentioned above.
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> P.S. fine to send this here, but you may be interested to know there 
>> is another mailing list specifically for ChimeraX questions: 
>> chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>
>>> On Oct 26, 2019, at 6:07 AM, Brown, Jeffrey <brownjw at wustl.edu 
>>> <mailto:brownjw at wustl.edu>> wrote:
>>> Hello,
>>>  I like a lot about ChimeraX; however, I can’t figure out how to 
>>> export to POV-RAY format. Has this functionality been removed?
>>>  Although there is a pseudo ray trace function in Chimera X - it is 
>>> impossible to add scenes like I did in this publication
>>> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009406
>>> In which I used Chimera to render all of the proteins and then moved 
>>> them around and added membrane etc.
>>> Also there is a lot more control in POV-RAY as it is code that you 
>>> can’t accidentally rotate with your mouse.
>>> Cheers,
>>> JWB
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