Hi Nick,
We're glad you like ChimeraX!

You can specify any color palette with "rainbow" (i.e. doesn't have to be a standard ROYGB palette).

Example:

rainbow /a palette darkblue:lightskyblue

With the "rainbow" command "palette" option you can specify a named palette or define it with 2 or more colors.  The simple example above uses 2 color names, but you can have more colors, and if they don't have names in ChimeraX, you can use hex codes, RGB, etc. as explained in the help.  See

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>

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 1, 2025, at 7:32 PM, Nick Matzke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX list,
>
> Thanks so much for this amazing software!
>
> I have a kind of obscure question for which I could not find an answer on Google.
>
> I've got the FliPQR-FlhB structure, from here:
> https://www.rcsb.org/structure/6S3L
>
> This has
>
> 5 copies FliP
> 1 copy FliR
> 4 copies FliQ
> 1 copy FlhB
>
> I opened it and am using ribbon view.
>
> I've colored the chains by protein type with these commands:
>
> color /a,b,c,d,e purple
> color /f red
> color /g,h,i,j green
> color /k yellow
>
> Now, I'd like to have each chain shaded from N-terminus to C-terminus, e.g. dark red to light red, or something like that. (I see the rainbow option, but this creates a very complex view if all 11 chains are each an roygbiv rainbow.)
>
> Almost as good, is there a way to easily label the N-terminus and C-terminus of each chain?
>
> Any suggestions!
>
> Thanks so much,
> Cheers,
> Nick