[Chimera-users] Capping in VRML

[Greg Couch]

HI Greg,

There's a good chance that the x3d2vrml program that comes with Chimera 
will work with the ChimeraX X3D output.  It only supports the subset of 
X3D that Chimera generates, but that might be enough.

The material problem with Chimera is due to a difference in how the 
colors are applied.  In one case, the base color is white, and the shape 
colors are given per-vertex.  And in the other case, the base color is 
the color of the shape and all vertices are the same color.  That's not 
possible to "fix" while preserving the color information.  If you don't 
care about the color information, then modifying the X3D file 
programmatically to make all of the materials the same is not hard.  X3D 
uses the XML syntax and Python has several packages that parse and write 
XML files.  So your pipeline would change to first save the output  in 
X3D, modify it using your Python program, and then run it through the 
x3d2vrml program to get your VRML output that you would input to Cinema 
4D.  I would expect the Python program to be at most 100 lines, perhaps 
less than 50.

     HTH,

     Greg

On 10/31/2020 3:01 PM, Greg Williams wrote:
> Oh dear…
>
> It’s distressing that you’ve lost the vrml export. That’s the only workable format I’ve been able to get out of Chimera and into Cinema 4D.
>
> There is no export in Chimera X that works well with Cinema 4D. I was able to export an obj file of 2bbv. The exported file was 300 mB! I was able to open it in C4D, but there was no content in the open file.
>
> I’ll do the best I can with the older Chimera. I’ve been hoping for several years that you would develop a good export function for modern commercial 3d graphics programs. I guess that’s not going to happen, and now I’ve lost VRML. Oh well….
>
> Thanks for the quick response.
>
> Greg
>
>
>
>> On Oct 31, 2020, at 1:22 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>> Hi Greg,
>> There's no setting like that (and Chimera only uses one material) so I believe it is simply a limitation or bug.  I'll make a ticket for this problem, but note that our group's resources are mainly directed toward ChimeraX these days.
>>
>> Can Cinema 4D read any of the other Chimera export formats?
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
>>
>> ChimeraX can save glTF, X3D, and some other 3D-object formats, but not currently VRML.  If one of those can be used as input to Cinema 4D, you might want to try ChimeraX instead.
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats>
>>
>> ChimeraX ribbons are calculated differently than Chimera, and there is a tube (curved cylinder) option for helices.  There are some ribbon choices in the Presets menu of ChimeraX, for those who aren't yet experienced with the commands and their options, and there are a few example images here:
>> <https://www.rbvi.ucsf.edu/chimerax/features.html#presets>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>> On Oct 31, 2020, at 11:02 AM, Greg Williams <gregoryw at comcast.net> wrote:
>>>
>>> When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material?
>>>
>>> Thanks!
>
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