Thanks very very much!! Cheers, Nick On Tue, Jun 3, 2025 at 7:16 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:

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