I don't know exactly what is in your structure, but you can use "color" with "target f" to color nucleotide representations whatever color you want. You can give residue number(s) to color the stubs or other nucleotide representations (tube, slab, etc.) of only specific residue(s).

See "simple coloring" commands:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

The default "bynucleotide" coloring uses standard residue names.  See "coloring by residue type":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#residue>

 You could either change the names of those residues to standard names, or you can just color them manually, i.e. with individual commands as mentioned above, or even add your own custom preset that includes whatever nonstandard names that tleap produces.

For this question seems like it would be easier to just try it yourself than to wait for an answer, but I'll try to answer below:
> Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ?

Yes, you can use * in residue names as mentioned here
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#wildcards>

...and change style using "nucleotides" command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.html>

However, if you want to change ALL of the nucleotide residues, it seems like you don't need to specify any residues, just do the whole structure, e.g.

open 1bna
nuc fill

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 Apr 23, 2024, at 8:14 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> P.S. I could partially fix the issue using the following command which reset the view.
> nucleotides ladder radius 0.4 showStubs true
>
> However, the first two sugar pairs are colored in grey compared to others (see another picture attached). Is it possible to change the color representation for the selected residues or alternatively implement some palettes presets for all of them at once ?
>
> Yours with thanks
>
> Enrico
>
>
> Il giorno mar 23 apr 2024 alle ore 12:01 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
> Dear Chimera-X users,
>
> I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)?
>
> Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ?
>
> Many thanks in advance !
>
> Enrico
> <test2.png>