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