How to use ColorBrewer palette?
Hello,
I would like to colour my structure with the ColorBrewer palette using ChimeraX. But I can't seem to get it to work. I used the command: color bychain cartoons;palette Pastel1-9. The error message displayed is "Unknown command: palette Pastel1-9." Could you help me with this please?
Many thanks, Tian
Hi Tian, When you put a semicolon (;) that means to start a new command. Instead you want the palette option as part of the color command.
Secondly, "color bychain" means to use a specific set of colors (shown in the following link) based on chain ID; it does not allow giving a different palette. https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#autocolors
Instead you want a command something like this:
rainbow chains palette Pastel1-9 target c
- OR (equivalently) -
color sequential chains palette Pastel1-9 target c
Target c (or target r) means cartoons only. As you may already know, the name of the palette is actually just Pastel1 but you can append -N where N is an integer in the range 3-9, meaning to use the first N colors in that palette. If you omit the -N it will use the default number of colors for that palette, 6.
See color sequential (rainbow) help https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential
See palette help https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options
See Colorbrewer palette colors and names https://rbvi.ucsf.edu/chimerax/docs/user/commands/palettes.html#colorbrewer
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 25, 2023, at 9:13 AM, Tianyang Liu (Staff) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I would like to colour my structure with the ColorBrewer palette using ChimeraX. But I can't seem to get it to work. I used the command: color bychain cartoons;palette Pastel1-9. The error message displayed is "Unknown command: palette Pastel1-9." Could you help me with this please? Many thanks, Tian
participants (2)
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Elaine Meng
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Tianyang Liu (Staff)