[chimerax-users] Bond between two sequential residues

[Elaine Meng]

Hi Derek,
Those are "chain trace" pseudobonds. 
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon).  That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown.  You could also hide the trace model with a command, e.g. if it is model #1.2, then

hide #1.1 model 

If you just instead used

hide #1.1

... that would not hide it at the model level, but all the pseudobonds in that model individually.  The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown.

hide @ca pseudobonds

... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.).

You could also close it

close #1.1

...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them.

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

> On Jul 16, 2020, at 3:19 PM, Derek Harris <derek.harris at aggiemail.usu.edu> wrote:
> 
> Hello,
> 
> When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
> 
> I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
> 
> 
> Derek Harris
> Postdoctoral Fellow
> Seefeldt Lab
> Department of Chemistry and Biochemistry
> Utah State University
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