[Chimera-users] Problem with nucleotide objects settings for 1d86

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 15 09:35:59 PDT 2021

Hi Saverio,
If you are trying to get a ladder rung that goes across the base pair, you would have to select both residues in the base pair.  E.g. in this case the base pair is 20.b with 5.a.  So you would need something like

command:  select :5.a,20.b

... and then use the menu like you did, or another command:

nuc side ladder sel

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

> On Mar 15, 2021, at 5:05 AM, svle at tiscali.it wrote:
> Hi,
> I have a visualization that seems not a correct one for 1d86 for DT  20.b when using
> Actions -> Atoms/Bonds -> nucleotide objects -> settings... .
> Settings:
> Show backbone as: Ribbon
> Show sides( .... ) as ladder
> Ladder Options:
> Ignore non-base H-bonds: false
> Shows stubs: false
> Rung radius: 0.45
> Using existing H-bonds: true
> In the png file the problem.
> Where I'm wrong?
> Thanks
> Saverio

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