Exporting 3D models from ChimeraX?
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-microso... Regards, Mikael
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@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-microso...
Regards, Mikael
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@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@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-microso...
Regards, Mikael
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Oli, As far as I know we go by the format descriptions rather than trying to evaluate the files in other applications, which may or may not have their own problems. Sometimes the format descriptions are not very complete, so different applications may interpret them differently, and I am sure that the exports from ChimeraX have some limitations. However, the short answer is that I don't know the reason for the color differences you are seeing. Maybe the others on the team with more detailed knowledge of the code can comment. Best, Elaine
On Oct 6, 2020, at 8:02 AM, Oliver Clarke <olibclarke@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@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@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-microso...
Regards, Mikael
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 <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@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@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@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-microso...
Regards, Mikael
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com> Kopio: ChimeraX Users Help <chimerax-users@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@gmail.com<mailto:olibclarke@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@cgl.ucsf.edu<mailto:meng@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@jyu.fi<mailto:mikael.p.karjalainen@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-microso... Regards, Mikael _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi! I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins... 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@cgl.ucsf.edu> Puolesta Karjalainen, Mikael Lähetetty: tiistai 6. lokakuuta 2020 21.25 Vastaanottaja: Tom Goddard <goddard@sonic.net>; Oliver Clarke <olibclarke@gmail.com> Kopio: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com<mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@gmail.com<mailto:olibclarke@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@cgl.ucsf.edu<mailto:meng@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@jyu.fi<mailto:mikael.p.karjalainen@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-microso... Regards, Mikael _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@jyu.fi> wrote:
Hi!
I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins... <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Karjalainen, Mikael Lähetetty: tiistai 6. lokakuuta 2020 21.25 Vastaanottaja: Tom Goddard <goddard@sonic.net>; Oliver Clarke <olibclarke@gmail.com> Kopio: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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 <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@gmail.com <mailto:olibclarke@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@cgl.ucsf.edu <mailto:meng@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 <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@jyu.fi <mailto:mikael.p.karjalainen@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-microso... <https://support.microsoft.com/en-us/office/3d-content-guidelines-for-microso...>
Regards, Mikael
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@sonic.net> Lähetetty: keskiviikko 7. lokakuuta 2020 0.21 Vastaanottaja: Karjalainen, Mikael <mikael.p.karjalainen@jyu.fi> Kopio: ChimeraX Users Help <chimerax-users@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@jyu.fi<mailto:mikael.p.karjalainen@jyu.fi>> wrote: Hi! I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins... 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@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Karjalainen, Mikael Lähetetty: tiistai 6. lokakuuta 2020 21.25 Vastaanottaja: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>>; Oliver Clarke <olibclarke@gmail.com<mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com<mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@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@gmail.com<mailto:olibclarke@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@cgl.ucsf.edu<mailto:meng@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@jyu.fi<mailto:mikael.p.karjalainen@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-microso... Regards, Mikael _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
Hi Mikael, I looked at the PyMol glTF, also way too bright in PowerPoint. It looks a little better than ChimeraX glTF in PowerPoint just because the PyMol colors are darker. By making the ChimeraX colors darker before writing glTF you can make a reasonable looking glTF in PowerPoint. Basically I took the ChimeraX normal bright colors and dimmed them a lot with color modify #1 lightness 10 before saving the glTF. Details are in the ChimeraX bug report. https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3810 This seems like simply a PowerPoint 3D lighting defect. This looks like some half-baked Microsoft effort -- the 3D model support was added in 2017 and still it has no usable control over lighting. I guess no one uses it. Tom ChimeraX glTF with lightness 10 in PowerPoint. Your PyMol glTF in PowerPoint:
On Oct 7, 2020, at 12:10 PM, Karjalainen, Mikael <mikael.p.karjalainen@jyu.fi> wrote:
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@sonic.net <mailto:goddard@sonic.net>> Lähetetty: keskiviikko 7. lokakuuta 2020 0.21 Vastaanottaja: Karjalainen, Mikael <mikael.p.karjalainen@jyu.fi> Kopio: ChimeraX Users Help <chimerax-users@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@jyu.fi <mailto:mikael.p.karjalainen@jyu.fi>> wrote:
Hi!
I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins... <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Karjalainen, Mikael Lähetetty: tiistai 6. lokakuuta 2020 21.25 Vastaanottaja: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>>; Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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 <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@gmail.com <mailto:olibclarke@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@cgl.ucsf.edu <mailto:meng@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 <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@jyu.fi <mailto:mikael.p.karjalainen@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-microso... <https://support.microsoft.com/en-us/office/3d-content-guidelines-for-microso...>
Regards, Mikael
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Hi Mikael, I tried putting a gltf model from ChimeraX 1.1 of PDB 2bna into PowerPoint (current Office 365 version: Version 2009 build 13231.20262) on Windows 10 and colors were faded as you saw due to completely wrong lighting. There is no lighting info in the glTF produced by ChimeraX and apparently PowerPoint chooses ridiculous bright ambient light making the colors nearly white and offers no way to change it other than editing the saved PowerPoint as described in the link you found. I edited the PowerPoint as described. There was one ambient light source and 3 point light sources all too bright. I turned down the brightness and added a black background using 3D Model Format options within PowerPoint and got better colors as shown below, but still not the saturated colors that are in the glTF file. Here are the powerpoint xml light settings I fiddled with. The color r,g,b values are on a scale of 1000000. Illuminance and intensity are given as a ratio n/d (who knows why, it is powerpoint). I reduced ambient 10 fold and point lights 2-fold. Also the point colors were all not white distorting the colors so I changed those (r,g,b). How the PowerPoint defaults can be so messed up I don't know. After changing those (I used emacs text editor) and reloading in powerpoint you need to rotate the model or it just shows the old lighting apparently having cached an image from before the changes. Still the colors are pastel while the file colors are fully saturated red, blue, yellow and green. Don't know why. <am3d:ambientLight> <am3d:clr><a:scrgbClr r="500000" g="500000" b="500000"/></am3d:clr> <am3d:illuminance n="10000" d="1000000"/> </am3d:ambientLight> <am3d:ptLight rad="0"> <am3d:clr><a:scrgbClr r="500000" g="500000" b="500000"/></am3d:clr> <am3d:intensity n="500000" d="1000000"/> <am3d:pos x="21959998" y="70920001" z="16344003"/> </am3d:ptLight> <am3d:ptLight rad="0"> <am3d:clr><a:scrgbClr r="500000" g="500000" b="500000"/></am3d:clr> <am3d:intensity n="500000" d="1000000"/> <am3d:pos x="-37964106" y="51130435" z="57631972"/> </am3d:ptLight> <am3d:ptLight rad="0"> <am3d:clr><a:scrgbClr r="500000" g="500000" b="500000"/></am3d:clr> <am3d:intensity n="500000" d="1000000"/> <am3d:pos x="-37739122" y="58056624" z="-34769649"/> </am3d:ptLight> Tom 2bna in ChimeraX ChimeraX glTF in PowerPoint Changed to black background in powerpoint with 3D Model Format options. Turned down lights and made the lights white.
On Oct 6, 2020, at 12:40 PM, Karjalainen, Mikael <mikael.p.karjalainen@jyu.fi> wrote:
Hi!
I found this one: https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins... <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Karjalainen, Mikael Lähetetty: tiistai 6. lokakuuta 2020 21.25 Vastaanottaja: Tom Goddard <goddard@sonic.net>; Oliver Clarke <olibclarke@gmail.com> Kopio: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Puolesta Tom Goddard Lähetetty: tiistai 6. lokakuuta 2020 20.29 Vastaanottaja: Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> Kopio: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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 <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@gmail.com <mailto:olibclarke@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@cgl.ucsf.edu <mailto:meng@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 <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@jyu.fi <mailto:mikael.p.karjalainen@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-microso... <https://support.microsoft.com/en-us/office/3d-content-guidelines-for-microso...>
Regards, Mikael
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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participants (4)
-
Elaine Meng -
Karjalainen, Mikael -
Oliver Clarke -
Tom Goddard