[chimerax-users] Bond between two sequential residues

[Elaine Meng]

Thanks Tom, I had forgotten about the autochain attribute!  

Here's the description of the "setattr" (set attribute) command, as well as a list of selected attributes and what they mean:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#model>

Elaine


> On Jul 17, 2020, at 9:19 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Derek,
> 
>   I see your problem is tricky because the chain trace pseudobonds are not created until the structure is displayed and needs them.  So you can't hide them until after they appear.  Here is the magic incantation to stop the chain trace pseudobonds from being created:
> 
> 	setattr #1 model autochain false
> 
>   Tom
> 
> 
> 
>> On Jul 16, 2020, at 7:16 PM, Derek Harris <derek.harris at aggiemail.usu.edu> wrote:
>> 
>> 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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