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#autocolor...> 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