Hide stubs with atom DNA backbones shown

open 9qj9

hide cartoon

~nuc /C:15 /D:23

hide /C:15 /D:23 & sideonly

  Tom

On Jan 28, 2026, at 2:09 PM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Tom! 

In this case it hides the whole residue (with backbone). I forgot to mention that I show DNA as atom spheres (not as cartoons!) so I need to hide only the side-chains which are not involved in interactions .. 

Yours with thanks

Enrico

Il giorno mer 28 gen 2026 alle ore 22:05 Tom Goddard <goddard@sonic.net> ha scritto:

You hide nucleotide stubs just like you hide atoms.  Here's an example

open 9qj9

hide /C:15 /D:23

  Tom

On Jan 28, 2026, at 9:21 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX users!

I have a question regarding the representation of DNA. 

In my input structure, the terminal base pairs are not involved in complementary pairing. When I display the entire DNA using atom activation stubs (with nucleotides ladder showStubs true), these terminal residues appear unconnected. I've tried hiding the stubs using the same command for selected terminal residues, but it also affects the entire DNA globally rather than just the terminal residues, e.g.:

nucleotides sel ladder showStubs false

How could I find the stubs for the selected residues only?

Many thanks in advance!

Enrico

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