Dear ChimeraX Development Team, I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization. I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image. I would like to formally request the introduction of a more robust solution that allows for the following: - The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). - Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements. Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features. Yours sincerely Enrico
The recommended way to add a background for a presentation image, for example a journal cover image, is to save your image from ChimeraX with a transparent background and then layer it on top of whatever image you want in a photo editor like Photoshop, or Gimp. Tom
On Oct 6, 2024, at 2:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Development Team,
I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization.
I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image.
I would like to formally request the introduction of a more robust solution that allows for the following:
The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements.
Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features.
Yours sincerely
Enrico
_______________________________________________ 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 actually would like to make a video for protein-RNA with a static background image of recent Nobel Prize laureates .. Il giorno lun 7 ott 2024 alle ore 20:15 Tom Goddard <goddard@sonic.net> ha scritto:
The recommended way to add a background for a presentation image, for example a journal cover image, is to save your image from ChimeraX with a transparent background and then layer it on top of whatever image you want in a photo editor like Photoshop, or Gimp.
Tom
On Oct 6, 2024, at 2:59 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Development Team,
I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization.
I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image.
I would like to formally request the introduction of a more robust solution that allows for the following:
- The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). - Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently.
These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements.
Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features.
Yours sincerely
Enrico _______________________________________________ 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/
Hi Enrico, To record a movie with an added background I suggest recording all the movie frames with transparency and then combining those frames with the background image to make a movie. Here is an example of how to do this. open 8of8 movie record dir ~/Desktop/movie transp true format png ; turn y 3 120 ; wait 120 ; movie stop # Let's put a cryoEM map in the background, open it and zoom in by hand open 16850 from emdb save ~/Desktop/movie/background.png Now to combine the transparent image frames and the background into a movie I'll use the ffmpeg movie encoder that comes with ChimeraX in a shell window. $ cd ~/Desktop/movie $ ~/Desktop/ChimeraX-1.8.app/Contents/bin/ffmpeg -loop 1 -i background.png -i chimovie_Umkk-%05d.png -filter_complex overlay=shortest=1 movie.mp4 Here is where I got this ffmpeg compositing trick https://stackoverflow.com/questions/10438713/overlay-animated-images-with-tr... Probably other movie making software can do this compositing too. Tom 
On Oct 8, 2024, at 5:33 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
I actually would like to make a video for protein-RNA with a static background image of recent Nobel Prize laureates ..
Il giorno lun 7 ott 2024 alle ore 20:15 Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> ha scritto:
The recommended way to add a background for a presentation image, for example a journal cover image, is to save your image from ChimeraX with a transparent background and then layer it on top of whatever image you want in a photo editor like Photoshop, or Gimp.
Tom
On Oct 6, 2024, at 2:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX Development Team,
I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization.
I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image.
I would like to formally request the introduction of a more robust solution that allows for the following:
The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements.
Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features.
Yours sincerely
Enrico
_______________________________________________ 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/
Enrico, this can be done using a video editor. There are many multi-track video editors you can use. Make your molecular video with a background colour that doesn't feature in your molecule, eg green or lilac. Put your still image in one track/layer in the video editor and place your ChimeraX video in a higher stack layer. Use a video filter such as chromakey (aka green screen) on the ChimeraX video clip so that the lilac or green colour in the background is subtracted (becomes transparent) revealing the still image underneath. Shotcut is a free, open source video editor with versions available for pc, mac and linux. Shotcut has lots of video filtering tools including chromakey. It works well with mp4 video clips and still images made with ChimeraX. Shotcut also has decent audio track editing and tools although the audio filters are not as powerful as say Audacity's. There are other video editors you can try, but we've had good results using Shotcut. There are many Shotcut tutorials online inc how to subtract video background using chromakey. Good luck. Scott _______________________________________ Dr Scott A. White SFHEA Email<mailto:s.a.white@bham.ac.uk> | LinkedIn<https://www.linkedin.com/in/scott-white-biosciences-uob/> | Canvas<https://canvas.bham.ac.uk/about/1539> Student Office Hours Please see my Canvas Profile<https://canvas.bham.ac.uk/about/1539> for drop-in times ______________________________________ ________________________________ From: Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 08 October 2024 13:33 To: Tom Goddard <goddard@sonic.net> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Images in background 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 actually would like to make a video for protein-RNA with a static background image of recent Nobel Prize laureates .. Il giorno lun 7 ott 2024 alle ore 20:15 Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> ha scritto: The recommended way to add a background for a presentation image, for example a journal cover image, is to save your image from ChimeraX with a transparent background and then layer it on top of whatever image you want in a photo editor like Photoshop, or Gimp. Tom On Oct 6, 2024, at 2:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX Development Team, I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization. I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image. I would like to formally request the introduction of a more robust solution that allows for the following: * The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). * Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements. Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features. Yours sincerely Enrico _______________________________________________ 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 (3)
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Enrico Martinez -
Scott White -
Tom Goddard