Get model chain color
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer
Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color. If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window. I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot. 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 Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer _______________________________________________ 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 Elaine, Is there a command to report the color of a selection in the log? A quick search in the help pages didn't turn up anything. Thank you, Guillaume ________________________________ From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Friday, June 13, 2025 5:27:25 PM To: Walshe, James Cc: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Get model chain color Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color. If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window. I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot. 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 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. [cid:af3b92a2-7013-4bb9-9d84-1296d7765f2e@user.uu.se]
On Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer _______________________________________________ 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/
_______________________________________________ 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/ 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
Thanks for the reminder! Yes, you can also use "info atomcolor" and "info rescolor" as mentioned in this earlier post: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> ... and in the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> That doesn't include nonatomic models, however. 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 Jun 13, 2025, at 8:50 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:
Hi Elaine,
Is there a command to report the color of a selection in the log? A quick search in the help pages didn't turn up anything. Thank you,
GuillaumeFrom: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Friday, June 13, 2025 5:27:25 PM To: Walshe, James Cc: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Get model chain color Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color.
If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window.
I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot.
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
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.
<Screenshot 2025-06-13 at 8.25.57 AM.png>
On Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer
Actually, you can use "info models" for nonatomic models to get their single colors, but it doesn't give a hex, instead RGBA in the ranget 0-255 for each component. For example, I had a density map #2: info models #2 attribute color ... giving in the Log: info models #2 attribute color model id #2 type Volume color 178,178,178,255 model id #2.1 type VolumeSurface color 225,178,250,255 The "Volume" one is if the map were shown as a semitransparent cloud, whereas the "VolumeSurface" one is the isosurface color. If you have some kind of multicoloring (by electrostatic potential etc.) this will not give it, it only gives the single-color assignment. Elaine
On Jun 13, 2025, at 9:29 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks for the reminder! Yes, you can also use "info atomcolor" and "info rescolor" as mentioned in this earlier post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
... and in the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>
That doesn't include nonatomic models, however.
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 Jun 13, 2025, at 8:50 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:
Hi Elaine,
Is there a command to report the color of a selection in the log? A quick search in the help pages didn't turn up anything. Thank you,
GuillaumeFrom: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Friday, June 13, 2025 5:27:25 PM To: Walshe, James Cc: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Get model chain color Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color.
If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window.
I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot.
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
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.
<Screenshot 2025-06-13 at 8.25.57 AM.png>
On Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer
_______________________________________________ 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 Elaine and Guillaume. info atomcolor was exactly what I was after! Best, James On 13.06.25, 18:37, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Actually, you can use "info models" for nonatomic models to get their single colors, but it doesn't give a hex, instead RGBA in the ranget 0-255 for each component. For example, I had a density map #2: info models #2 attribute color ... giving in the Log: info models #2 attribute color model id #2 type Volume color 178,178,178,255 model id #2.1 type VolumeSurface color 225,178,250,255 The "Volume" one is if the map were shown as a semitransparent cloud, whereas the "VolumeSurface" one is the isosurface color. If you have some kind of multicoloring (by electrostatic potential etc.) this will not give it, it only gives the single-color assignment. Elaine
On Jun 13, 2025, at 9:29 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Thanks for the reminder! Yes, you can also use "info atomcolor" and "info rescolor" as mentioned in this earlier post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>/message/JTCP2OSUVVFHYYWPFIKSDOYULTGJQSAD/>
... and in the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>>
That doesn't include nonatomic models, however.
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 Jun 13, 2025, at 8:50 AM, Guillaume Gaullier <http://guillaume.ga <mailto:guillaume.gaullier@kemi.uu.se>> wrote:
Hi Elaine,
Is there a command to report the color of a selection in the log? A quick search in the help pages didn't turn up anything. Thank you,
GuillaumeFrom: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Sent: Friday, June 13, 2025 5:27:25 PM To: Walshe, James Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Get model chain color Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color.
If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window.
I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot.
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
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.
<http://Screenshot2025-06-13at8.25.57AM.png>
On Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de <mailto:james.walshe@mpinat.mpg.de> | https://www.mpinat.mpg.de/cramer <https://www.mpinat.mpg.de/cramer>
_______________________________________________ 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 <mailto:chimerax-users@cgl.ucsf.edu>/
Thank you, good to know! I was looking wrongly into options to the "color" command, but didn't think to look at "info". Cheers, Guillaume ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, June 13, 2025 6:37:30 PM To: "chimerax-users@cgl.ucsf…"; Elaine Meng Cc: Guillaume Gaullier; Walshe, James Subject: Re: [chimerax-users] Get model chain color Actually, you can use "info models" for nonatomic models to get their single colors, but it doesn't give a hex, instead RGBA in the ranget 0-255 for each component. For example, I had a density map #2: info models #2 attribute color ... giving in the Log: info models #2 attribute color model id #2 type Volume color 178,178,178,255 model id #2.1 type VolumeSurface color 225,178,250,255 The "Volume" one is if the map were shown as a semitransparent cloud, whereas the "VolumeSurface" one is the isosurface color. If you have some kind of multicoloring (by electrostatic potential etc.) this will not give it, it only gives the single-color assignment. Elaine
On Jun 13, 2025, at 9:29 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks for the reminder! Yes, you can also use "info atomcolor" and "info rescolor" as mentioned in this earlier post:
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
... and in the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>
That doesn't include nonatomic models, however.
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 Jun 13, 2025, at 8:50 AM, Guillaume Gaullier <guillaume.gaullier@kemi.uu.se> wrote:
Hi Elaine,
Is there a command to report the color of a selection in the log? A quick search in the help pages didn't turn up anything. Thank you,
GuillaumeFrom: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Friday, June 13, 2025 5:27:25 PM To: Walshe, James Cc: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Get model chain color Hi James, There are several dialogs with a square "color well" showing the current color of something, and you can just click the color well to bring up the system color editor. In the color editor (system-dependent as to how exactly it looks) there is generally some way to see the hex code or RGBA values of the color.
If it's the whole-model color, you can click the color well in the Models list. Or if it is some specific residue's ribbon segment or specific atom, you can select that ribbon segment or atom, and then open the Selection Inspector and inspect that kind of item (Atoms, Residues, etc.) properties to show the corresponding color well. You can open the Selection Inspector with menu: Actions... Inspect, or click the green magnifying glass icon in the Home toolbar which is normally across the top of the window.
I'm on a Mac so when I click a color well I get something like what is shown in the attached screenshot.
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
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.
<Screenshot 2025-06-13 at 8.25.57 AM.png>
On Jun 13, 2025, at 7:29 AM, Walshe, James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, Is there an easy way to get the color code for a model? Or a specific chain of that model? Let’s say I really like the default colors a model is loaded with and I want to find the exact hexa color code for each chain? Thanks! Dr James Walshe | Postdoctoral Researcher | Cramer Group Department of Molecular Biology | Max Planck Institute for Multidisciplinary Sciences | Am Fassberg 11 37077 Göttingen, Germany T: +49 551 201-2807 | E: james.walshe@mpinat.mpg.de | https://www.mpinat.mpg.de/cramer
_______________________________________________ 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/
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. 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
participants (3)
-
Elaine Meng -
Guillaume Gaullier -
Walshe, James