Opening chimera within MS powerpoint
Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, Sorry, I don't know anything about Powerpoint, but I doubt it. I know that years ago people used to first make a movie file with Chimera and then put the pre-made movie in their Powerpoint, but it would not be interactive. Personally I would just make a ChimeraX session and then put a link in the Powerpoint to the session file, which (maybe?) if you click it would start the ChimeraX session. I make all my presentations in HTML and do something like that, but I don't use Powerpoint. Even starting ChimeraX may take more time than you want, so another approach I've taken in the past is just to have the session already started and simply put a slide in the presentation that reminds me to change apps and show the already-started ChimeraX session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 8, 2024, at 6:37 AM, Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ Chimera-users mailing list --chimera-users@cgl.ucsf.edu To unsubscribe send an email tochimera-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Thank you Elaine and Greg for your responses! On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides.
-- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Prathvi, I know this isn't answering directly your question, but might be useful. Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result. Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands. Or perhaps others have a good tip for lighting settings... One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop. Scott _______________________________________ Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534 Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________ ________________________________ From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses! On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote: Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu<mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes. Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post. It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned: (A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify> I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.) (B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...> There was also this post suggesting that transparency doesn't work either: <https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-...> 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 8, 2024, at 2:24 AM, Scott White via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
I tried exporting a rainbow colored ribbon of 1ubq as GLTF from today's ChimeraX daily build and opening in PowerPoint for Mac version 16.83 (24031120) part of Microsoft 365, and the colors looked nearly the same in PowerPoint as in ChimeraX. Meghan McCarthy tried the same and her PowerPoint colors looked very different -- I have not heard what version of PowerPoint she was using. At any rate, it may be that newer versions of PowerPoint don't have the lighting problem with GLTF models. Tom Image of 1ubq rainbow snapshot from ChimeraX daily build. Image of GLTF exported from ChimeraX in PowerPoint without any adjustments GLTF file from ChimeraX used in above two images
On Apr 8, 2024, at 9:58 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes.
Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post.
It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned:
(A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify>
I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.)
(B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
There was also this post suggesting that transparency doesn't work either: <https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-...>
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 8, 2024, at 2:24 AM, Scott White via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
thanks everyone. Have tried several of the suggestions. The gltf for a rainbow-coloured ribbon is certainly usable, and much better (with the most recent ChimeraX version) than my earlier attempts. I'm not getting as good a result as Tom posted - the helices are not as crisp. That's probably down to my graphics card or PowerPoint version rather than ChimeraX. But for conveying the 3D structure of the protein in PowerPoint using the gltf/glb format can often be better than showing a flat, still image. thanks! Scott _______________________________________ Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534 Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________ ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: 09 April 2024 02:24 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Scott White (Biosciences) <s.a.white@bham.ac.uk>; Prathvi Singh <prathvi@iitk.ac.in>; Elaine Meng <meng@cgl.ucsf.edu>; McCarthy, Meghan (NIH/NIAID) [C] <meghan.mccarthy@nih.gov> Subject: Re: [chimerax-users] Embedding 3D within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. I tried exporting a rainbow colored ribbon of 1ubq as GLTF from today's ChimeraX daily build and opening in PowerPoint for Mac version 16.83 (24031120) part of Microsoft 365, and the colors looked nearly the same in PowerPoint as in ChimeraX. Meghan McCarthy tried the same and her PowerPoint colors looked very different -- I have not heard what version of PowerPoint she was using. At any rate, it may be that newer versions of PowerPoint don't have the lighting problem with GLTF models. Tom Image of 1ubq rainbow snapshot from ChimeraX daily build. [cid:e708b92e-fabf-4eb5-883b-c4005013fad1@GBRP265.PROD.OUTLOOK.COM] Image of GLTF exported from ChimeraX in PowerPoint without any adjustments [cid:a06ccce0-44a8-4d3a-af8a-01b5f637f1b7@GBRP265.PROD.OUTLOOK.COM] GLTF file from ChimeraX used in above two images
On Apr 8, 2024, at 9:58 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes.
Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post.
It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned:
(A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify>
I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.)
(B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
There was also this post suggesting that transparency doesn't work either: <https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-...>
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 8, 2024, at 2:24 AM, Scott White via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
I used ChimeraX-1.7.1 (the latest stable version) to save my protein as a 3D model in GLB format and loaded it in powerpoint and I must say the 3D model looks breathtaking, complete with dynamic shadows. If only there was a powerpoint plugin that could allow atom/residue/chain/model selection and changing their displays to sticks, surfaces, etc. On Tue, Apr 9, 2024 at 6:54 AM Tom Goddard <goddard@sonic.net> wrote:
I tried exporting a rainbow colored ribbon of 1ubq as GLTF from today's ChimeraX daily build and opening in PowerPoint for Mac version 16.83 (24031120) part of Microsoft 365, and the colors looked nearly the same in PowerPoint as in ChimeraX. Meghan McCarthy tried the same and her PowerPoint colors looked very different -- I have not heard what version of PowerPoint she was using. At any rate, it may be that newer versions of PowerPoint don't have the lighting problem with GLTF models.
Tom
Image of 1ubq rainbow snapshot from ChimeraX daily build.
Image of GLTF exported from ChimeraX in PowerPoint without any adjustments
GLTF file from ChimeraX used in above two images
On Apr 8, 2024, at 9:58 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes.
Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post.
It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned:
(A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify>
I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.)
(B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread < https://urldefense.proofpoint.com/v2/url?u=https-3A__answers.microsoft.com_e...
There was also this post suggesting that transparency doesn't work either: < https://urldefense.proofpoint.com/v2/url?u=https-3A__answers.microsoft.com_e...
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 8, 2024, at 2:24 AM, Scott White via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
At this point, you are better off preparing a figure in ChimeraX and pasting the picture in your slide, or using ChimeraX interactively during the presentation with commands prepared in advance (optionally wrapped into an html file that you open from ChimeraX, so you only need to click links to execute arbitrarily complex series of commands) like Elaine described in a recent discussion. I got excited about 3D models in Powerpoint when first reading this discussion, then I tried it and noticed that Powerpoint doesn’t let you rotate the model in presentation mode. This makes this feature much less useful for the use case I envisioned. It could be a great feature to answer questions at the end of a talk: the model as displayed doesn’t quite show the region related to the question? simply rotate and zoom right from your slideshow! that would be super convenient. Or does it do it and I simply couldn’t figure out how? If so, I’d love to know. Cheers, Guillaume On 9 Apr 2024, at 09:02, Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: I used ChimeraX-1.7.1 (the latest stable version) to save my protein as a 3D model in GLB format and loaded it in powerpoint and I must say the 3D model looks breathtaking, complete with dynamic shadows. If only there was a powerpoint plugin that could allow atom/residue/chain/model selection and changing their displays to sticks, surfaces, etc. On Tue, Apr 9, 2024 at 6:54 AM Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: I tried exporting a rainbow colored ribbon of 1ubq as GLTF from today's ChimeraX daily build and opening in PowerPoint for Mac version 16.83 (24031120) part of Microsoft 365, and the colors looked nearly the same in PowerPoint as in ChimeraX. Meghan McCarthy tried the same and her PowerPoint colors looked very different -- I have not heard what version of PowerPoint she was using. At any rate, it may be that newer versions of PowerPoint don't have the lighting problem with GLTF models. Tom Image of 1ubq rainbow snapshot from ChimeraX daily build. Image of GLTF exported from ChimeraX in PowerPoint without any adjustments GLTF file from ChimeraX used in above two images
On Apr 8, 2024, at 9:58 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes.
Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post.
It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned:
(A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify>
I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.)
(B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-inside-powerpoint/d0c0c316-8019-4c25-b0f6-86500e512f91<https://urldefense.proofpoint.com/v2/url?u=https-3A__answers.microsoft.com_en-2Dus_msoffice_forum_all_3d-2Dmodel-2Dlighting-2Dinside-2Dpowerpoint_d0c0c316-2D8019-2D4c25-2Db0f6-2D86500e512f91&d=DwMFaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=x4JSVCR6_B_JWXoFcnd0yguTXqcI2o0dj3bXi_yDu94zFpb17rd666_hRo1REY5A&s=tztbQ_zljYxA0vqyW0mHqhJkDyJHEm_Nx_SMXbcw-cQ&e=>>
There was also this post suggesting that transparency doesn't work either: <https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-but-doesnt-support/002d1f4e-061d-4ab6-a692-ed217945724a<https://urldefense.proofpoint.com/v2/url?u=https-3A__answers.microsoft.com_en-2Dus_msoffice_forum_all_powerpoint-2Duses-2Dgltf-2Dbut-2Ddoesnt-2Dsupport_002d1f4e-2D061d-2D4ab6-2Da692-2Ded217945724a&d=DwMFaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=cL0WvLW074DHXNhkYyxmeHhSv30WxTDLNOf7i2e1T40&m=x4JSVCR6_B_JWXoFcnd0yguTXqcI2o0dj3bXi_yDu94zFpb17rd666_hRo1REY5A&s=UjHDzyWumElec-co5c6_LYpYlJsHsQ_sdxFFTkx5ftw&e=>>
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 8, 2024, at 2:24 AM, Scott White via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Tom, My comparison was of a model directly exported from ChimeraX and a ChimeraX workflow coming out of NIH 3D. The NIH 3D workflows was washed out. Can you please download the glb for the rainbow ribbon model here and compare? I am using the latest version of PPT on a PC. https://3d.nih.gov/entries/3DPX-000133 Thanks Meghan From: Tom Goddard <goddard@sonic.net> Sent: Monday, April 8, 2024 9:25 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Scott White <s.a.white@bham.ac.uk>; Prathvi Singh <prathvi@iitk.ac.in>; Elaine Meng <meng@cgl.ucsf.edu>; McCarthy, Meghan (NIH/NIAID) [C] <meghan.mccarthy@nih.gov> Subject: [EXTERNAL] Re: [chimerax-users] Embedding 3D within MS powerpoint I tried exporting a rainbow colored ribbon of 1ubq as GLTF from today's ChimeraX daily build and opening in PowerPoint for Mac version 16.83 (24031120) part of Microsoft 365, and the colors looked nearly the same in PowerPoint as in ChimeraX. Meghan McCarthy tried the same and her PowerPoint colors looked very different -- I have not heard what version of PowerPoint she was using. At any rate, it may be that newer versions of PowerPoint don't have the lighting problem with GLTF models. Tom Image of 1ubq rainbow snapshot from ChimeraX daily build. CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. [cid:image001.png@01DA8A6D.4E76AE40] Image of GLTF exported from ChimeraX in PowerPoint without any adjustments [cid:image002.png@01DA8A6D.4E76AE40] GLTF file from ChimeraX used in above two images
On Apr 8, 2024, at 9:58 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Thanks, Scott! Regarding the problem of poor Powerpoint lighting of GLTF (GLB) files, this was discussed at a recent meeting where I was trying to take notes.
Chimera does not output this format, only ChimeraX, so I'm just including the chimerax-users list on this post.
It was difficult to keep up with the discussion and I have not tried any of these solutions myself, but to the best of my recollection these two approaches were mentioned:
(A) before exporting GLB from ChimeraX, shifting the colors in ChimeraX to compensate using ChimeraX command "color modify" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#modify>
I'd written "lightness" as the modification in the notes, but not sure I heard the discussion correctly, so it might be one of the other options (saturation, whiteness, etc.)
(B) "hacking" Powerpoint itself to delete its poor lighting as per the answer in this thread <https://answers.microsoft.com/en-us/msoffice/forum/all/3d-model-lighting-ins...>
There was also this post suggesting that transparency doesn't work either: <https://answers.microsoft.com/en-us/msoffice/forum/all/powerpoint-uses-gltf-...>
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 8, 2024, at 2:24 AM, Scott White via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote:
Prathvi,
I know this isn't answering directly your question, but might be useful.
Aside from making and inserting a short .mp4 movie into your PowerPoint, the newer versions of PowerPoint now allow insertion of rotatable 3D objects (PowerPoint > Insert > 3D Models > your-file.glb). It's ok if all you want is a short 360 degree spin (PowerPoint > Animations > Turntable) or a rock'n'roll (PowerPoint > Animations > Swing). The main issue is the default lighting when exporting glb files from ChimeraX is far from optimal for this purpose, although showing your model in sphere style can be "usable". Inserting an mp4 movie still gives a more satisfying result.
Inserting glb files downloaded from Sketchfab works very well with PowerPoint, so it is the glb from ChimeraX that gives less than optimal results, at least in my hands.
Or perhaps others have a good tip for lighting settings...
One note of caution - if using rotatable glb files in your PowerPoint presentation, make sure the lectern computer in the lecture theatre has a compatible version of PowerPoint - or always use your own laptop.
Scott
_______________________________________
Dr Scott A. White SFHEA School of Biosciences, Room T716 University of Birmingham, B15 2TT E: s.a.white@bham.ac.uk<mailto:s.a.white@bham.ac.uk> T: +44-(0)121-414-7534
Office Hours Generally Tues 10am - 11am, Wed 3 pm - 4 pm Please contact me for an appointment. ______________________________________
From: Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: 05 April 2024 12:09 To: Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] Re: [Chimera-users] Opening chimera within MS powerpoint CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Thank you Elaine and Greg for your responses!
On Sat, Mar 9, 2024 at 5:08 AM Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> wrote: If you can put your presentation on a web page, ChimeraX's help command can display that web page in the help viewer. And that web page could have embedded ChimeraX commands that control ChimeraX. Look at the ChimeraX tutorials for examples of how it's done. So not Microsoft Powerpoint, but maybe Google Slides. -- Greg On 3/8/2024 6:37 AM, Prathvi Singh via Chimera-users wrote:
Hi Elaine,
I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)?
This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation.
Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (7)
-
Elaine Meng -
Greg Couch -
Guillaume Gaullier -
McCarthy, Meghan (NIH/NIAID) [C] -
Prathvi Singh -
Scott White -
Tom Goddard