[chimerax-users] How to make nucleotides same color?

[Elaine Meng]

Hi Visvaldas,
Currently you can't change the default without changing the code, but you could just color them blue after opening the structure, e.g. command:

color nucleic blue target f

... or for the same shade of blue as in Chimera, 

color nucleic #3050f8 target f

("f" is for ring fill which also works for nucleotide representations)  You could make an alias or a custom preset if you don't want to remember command(s) but it would still require entering the alias or specifying your custom preset from the menu.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>

If simple is what you want, perhaps easier is to just show stubs (broken ladder rungs) or ladder rungs.  You can do that by going to the Nucleotides tab of the toolbar (across the top) and clicking the corresponding icon, or with commands, e.g.

nuc stubs
nuc ladder

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.html>

Actually there are several differences other than color.  Chimera also showed the ribose and "nubs" on the slabs to show orientation.  You can do all those things with the "nucleotides" command if you want, e.g.

nuc slab showOrientation true

... which could be part of your custom preset if you make one.  However, I don't think you can make the ribose ring fill coloring the same as in Chimera, where  each "wedge" matches its perimeter atom, because in Chimera, the ring fill will instead be the same color as the slab.

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, 2021, at 1:23 PM, Visvaldas K. via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I couldn't find how to change the default coloring of the nucleotides in ChimeraX. I'd like the color of all nucleotides to be blue like in the "old" Chimera: multiple colors distract from the details I am trying to convey. Is it possible?
> Best regards,
> Visvaldas
> edu/mailman/listinfo/chimerax-users