[chimerax-users] DNA/RNA ribbon in ChimeraX

[Elaine Meng]

Dear Chongzhao You,
The calculation of ribbon path (where the center of the ribbon goes in 3D) is different in ChimeraX than in Chimera.  The calculation in ChimeraX does not have any ribbon spline options, sorry.

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

For RNA and DNA, the ChimeraX ribbon follows the C5' atoms: the center of the ribbon will pass through the exact positions of the C5' atom of each residue.  Although you can change the cross-section shape and width/height of the ribbon with the  command "cartoon style" (same as "ribbon style"), 

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

....the only way I can think of to change the path is to use different atoms. Although the cartoon/ribbon command does not have an option to use different atoms, you can just hide the ribbon, and instead use command "shape tube" or "shape ribbon" with whatever atoms you like, for example:

open 359d
hide ribbons
shape tube nucleic & @P
hide backbone

Shape commands:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#tube>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#ribbon>

One disadvantage is that the sticks from the simplified "nucleotide" representations of the DNA/RNA bases may not connect well with the tube or ribbon from the "shape" command.  You could show atoms instead, for example, continuing from the command examples above:

~nucleotide
show ribose

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 24, 2023, at 3:03 AM, 游宠昭 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear developers,
>   Sorry to bother you. Recently, I notice that chimera x display the DNA/RNA in a different way from that in chimera, and I find that there is a option in chimera called ribbon spline containing two options:B-spline and cardinal which explain why DNA/RNA is displayed in different ways in two softwares.
> 
>   However, I can not find the related actions in chimera x: "ribbon spline" in chimera refers to what in chimera x and how can I adjust this parameter.
> Sincerely,
> Chongzhao You