If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command?
David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892
Email: dmargulies@niaid.nih.govmailto:dmargulies@niaid.nih.gov, dhm@nih.govmailto:dhm@nih.gov Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd
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Hi David, Commands "info atomcolor" "info rescolor" etc. were added recently to report colors as hex codes. I.e. I believe you would need a recent daily build to have these commands. Examples:
info atomcolor /A:54@ca info rescolor sel
...where "sel" means current selection. See "info" command help: https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html
There are also older ways (included in production release) via the GUIs. For any coloring, whether bychain or other method:
If you select some atom or ribbon segment that has the color, then you can open Selection Inspector (menu Actions... Inspect or by clicking the green magnifying glass icon), and in that dialog inspect atoms or residues (for cartoon or ribbon color), and click the square color well to open the system color editor dialog. The system color editor dialog will generally show RGB components and hex code for the color.
Selection Inspector: https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html
If it's one of the stereotyped color sets like bychain, there are also help pages that show the color in tables and mousing over the table cell shows in a pop-up the color name or other designation such as r,g,b if it is not a built-in color name.
E.g. see the bychain colors here: https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#autocolors
For the built-in color names, hex codes and r,g,b components are given directly in a table: https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 1:44 PM, Margulies, David (NIH/NIAID) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command?
David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892
Email: dmargulies@niaid.nih.gov, dhm@nih.gov Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd
“Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-of...
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Thanks very much, Elaine. I had found some of these, but the info commands are the best. The mousing over sometimes works, sometimes doesn’t, not sure why.
D
David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892
Email: dhm@nih.govmailto:dhm@nih.gov Ph: 301-496-6429 Fax: 301-480-7352 Web: https://irp.nih.gov/pi/david-margulies
“Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – Executive Order 12674 (https://ethics.od.nih.gov/EO12674)
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From: Elaine Meng meng@cgl.ucsf.edu Date: Thursday, September 28, 2023 at 8:36 PM To: Margulies, David (NIH/NIAID) [E] dmargulies@niaid.nih.gov Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Color info Hi David, Commands "info atomcolor" "info rescolor" etc. were added recently to report colors as hex codes. I.e. I believe you would need a recent daily build to have these commands. Examples:
info atomcolor /A:54@ca info rescolor sel
...where "sel" means current selection. See "info" command help: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>
There are also older ways (included in production release) via the GUIs. For any coloring, whether bychain or other method:
If you select some atom or ribbon segment that has the color, then you can open Selection Inspector (menu Actions... Inspect or by clicking the green magnifying glass icon), and in that dialog inspect atoms or residues (for cartoon or ribbon color), and click the square color well to open the system color editor dialog. The system color editor dialog will generally show RGB components and hex code for the color.
Selection Inspector: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html>
If it's one of the stereotyped color sets like bychain, there are also help pages that show the color in tables and mousing over the table cell shows in a pop-up the color name or other designation such as r,g,b if it is not a built-in color name.
E.g. see the bychain colors here: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#autocolors>
For the built-in color names, hex codes and r,g,b components are given directly in a table: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 1:44 PM, Margulies, David (NIH/NIAID) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command?
David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892
Email: dmargulies@niaid.nih.gov, dhm@nih.gov Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd
“Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.federa...https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-of-ethical-conduct-for-employees-of-the-executive-branch-amendments-to-the-seeking-other
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participants (2)
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Elaine Meng -
Margulies, David (NIH/NIAID) [E]