[chimerax-users] Exporting 3D models from ChimeraX?

Wed Oct 7 12:10:12 PDT 2020

Hi!

I sent gltf file from PyMol via Chimera’s bug menu. I remembered it wrong and it was not perfect. Colours are washed out, but not so badly? Model had much deeper colours in PyMol than in Chimera.

Regards,
Mikael

Lähettäjä: Tom Goddard <goddard at sonic.net>
Lähetetty: keskiviikko 7. lokakuuta 2020 0.21
Vastaanottaja: Karjalainen, Mikael <mikael.p.karjalainen at jyu.fi>
Kopio: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Aihe: Re: [chimerax-users] Exporting 3D models from ChimeraX?

Hi Mikael,

  Probably the washed out colors is something easy to fix in ChimeraX.  Could you use ChimeraX menu Help / Report a Bug and attach the gltf from PyMol that has nice colors and I can look at that file and see what extra stuff it is putting in, probably some material setting is needed.

  The ChimeraX residue or atom labels that always face you as you rotate the model are not supported in the glTF format as far as I can see.

                             Tom

On Oct 6, 2020, at 12:40 PM, Karjalainen, Mikael <mikael.p.karjalainen at jyu.fi<mailto:mikael.p.karjalainen at jyu.fi>> wrote:

Hi!

I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-inside-powerpoint/d0c0c316-8019-4c25-b0f6-86500e512f91

Problem can be lighting in powerpoint and you can remove it by editing .pptx file. I tried and I got first black 3D model and then slightly better (I didn’t remove "am3d:ambientLight"). For me this didn’t fix the colors. I tried with PyMol and it’s glTF file works. Maybe there is something which could be changed in ChimeraX.

Regards,
Mikael

Lähettäjä: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu<mailto:chimerax-users-bounces at cgl.ucsf.edu>> Puolesta Karjalainen, Mikael
Lähetetty: tiistai 6. lokakuuta 2020 21.25
Vastaanottaja: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>; Oliver Clarke <olibclarke at gmail.com<mailto:olibclarke at gmail.com>>
Kopio: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Aihe: Re: [chimerax-users] Exporting 3D models from ChimeraX?

Hi!

Thank you! It was too easy to save to glb format that I didn’t realize how to do it.

Colors are washed out and I didn’t find any fix to it. I tried some 3d software which come with Windows 10 and tried to save glb file with dimmer colors. Also, I noticed that labels are just flat sheets, if I have them in structure (Can I get floating 2D text which would always face to the viewer?). If someone has easy solution for this colors issue, I would be happy to hear it.

Regards,
Mikael

Lähettäjä: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu<mailto:chimerax-users-bounces at cgl.ucsf.edu>> Puolesta Tom Goddard
Lähetetty: tiistai 6. lokakuuta 2020 20.29
Vastaanottaja: Oliver Clarke <olibclarke at gmail.com<mailto:olibclarke at gmail.com>>
Kopio: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Aihe: Re: [chimerax-users] Exporting 3D models from ChimeraX?

Hi Oli,

  The core glTF format does not support lighting.  It also does not specify a background color as far as I can tell, here is the specification

https://github.com/KhronosGroup/glTF/blob/master/specification/2.0/README.md

For the washed out colors, one problem we have seen before is that macOS uses a special Apple color profile which is not sRGB and if that is not preserved the colors are faded it.  glTF does not appear to have support for color profiles.  Another possibility is that the default material in glTF fades the colors.  ChimeraX does not export material information into the glTF file.  Also glTF can handle camera positions but ChimeraX does not include that.

  ChimeraX exports the shapes and vertex colors.  It is primarily used to get models into general 3D packages like Blender, Cinema4D, Maya, where the materials, camera angles, lighting model can all be set as needed for the end application.

  Despite the many limitations of the glTF format and what ChimeraX puts into it, other formats like OBJ and STL are much more severely limited, neither supports vertex colors that ChimeraX uses.  STL does not support any colors, just a list of triangles.

                             Tom

On Oct 6, 2020, at 8:02 AM, Oliver Clarke <olibclarke at gmail.com<mailto:olibclarke at gmail.com>> wrote:

Hi Elaine - I just tried this and it saves as glb, but importing into powerpoint gives washed out colors - it doesn't seem to preserve any lighting options - and the background color is not preserved. I guess this is an issue on Microsoft's end though?

Oli

On Oct 6, 2020, at 10:52 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Mikael,
ChimeraX can save glb, stl, obj, etc. The save formats are listed in the User Guide help page for "save":

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats>

... or you can list them in the Log with command "save formats."
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 6, 2020, at 2:14 AM, Karjalainen, Mikael <mikael.p.karjalainen at jyu.fi<mailto:mikael.p.karjalainen at jyu.fi>> wrote:

Hi!
Is it possible to export 3D models from ChimeraX? Preferably in formats GLB (best for powerpoint), FBX, OBJ or 3MF? You can in old Chimera, but for powerpoint presentations it can only give STL files which do not have textures.

Here are supported file formats for Office products: https://support.microsoft.com/en-us/office/3d-content-guidelines-for-microsoft-03a7b493-d549-4f1a-9735-f2457adf6261

Regards,
Mikael

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