[chimerax-users] Bond between two sequential residues

[Derek Harris]

Thank you Elaine for the detailed response. While all of these options work
as intended, they don't quite seem to solve my problem. In my movie I am
hiding a selection and then reshowing it. While it is hidden I can't
control the pseudobonds and I can't seem to hide them in a single line
command without a wait 1, which shows them for that 1s. Am I missing
something or is this just something I need to work around?

Derek Harris
Postdoctoral Fellow
Seefeldt Lab
Department of Chemistry and Biochemistry
Utah State University


On Thu, Jul 16, 2020 at 4:42 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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>
>
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