Re: [chimerax-users] palettes and color keys
A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes. Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland -----Original Message----- From: chimerax-users-request@cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 12. huhtikuutata 2022 22:00 To: chimerax-users@cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 15 Send ChimeraX-users mailing list submissions to chimerax-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request@cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."
Hi Martti, Sorry no, the Color Key only allows drawing one at a time in the graphics window. Currently the workaround is to draw the other one in a blank window and then use some other image-editing program (gimp, photoshop) to put the two images together. Since Chimera allows using an image as the background, you could make a figure with 2 color keys by first making a blank window image except with one color key, and then using that image as the background of the Chimera graphics window while showing the structure and another color key. However, ChimeraX does not currently have the option of using an arbitrary image as the background. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 18, 2022, at 11:14 PM, Martti Tolvanen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes.
Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland
Hi Elaine, The image editing option to add the second color key sounds like the best option here. Thanks, -Martti -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: 19. huhtikuutata 2022 19:48 To: Martti Tolvanen <martti.tolvanen@utu.fi> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] palettes and color keys Hi Martti, Sorry no, the Color Key only allows drawing one at a time in the graphics window. Currently the workaround is to draw the other one in a blank window and then use some other image-editing program (gimp, photoshop) to put the two images together. Since Chimera allows using an image as the background, you could make a figure with 2 color keys by first making a blank window image except with one color key, and then using that image as the background of the Chimera graphics window while showing the structure and another color key. However, ChimeraX does not currently have the option of using an arbitrary image as the background. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 18, 2022, at 11:14 PM, Martti Tolvanen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes.
Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland
participants (2)
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Elaine Meng -
Martti Tolvanen