[Chimera-users] longbond command documentation?

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 6 10:14:49 PDT 2017


Hi Oli,
The longbond documentation is up to date — namely, our expectation is that when TER cards are missing, then pseudobonds (not bonds) are generated and shown in Chimera.  However, there may be something specific about your structure, or another issue I’ve seen is that when I’ve hidden some backbone atoms (not missing in my case), the autochaining can make some ugly long bonds.  So besides

~longbond

to hide missing-segment pseudobonds, you might also try turning autochaining off for the model:

setattr m autochain 0

This molecule model attribute is also listed in the Selection Inspector GUI.  Other than that, the only other idea is to individually specify/delete the bonds you don’t want with the command ~bond or in the Build Structure GUI, Adjust Bonds "delete selected bonds" option.

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

> On Sep 6, 2017, at 8:45 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi,
> I want to use the longbond command to clean up display of a PDB file which has some ugly bits – missing TER cards etc - and which hence has unphysical bonds displayed. 
>  
> According to the manual `longbond` should be the command to use, but it doesn’t seem to work – it just displays and undisplays pseudobonds. 
>  
> If I attempt to use arguments as described in the docs, I get a message saying that longbond no longer takes arguments. Is there an updated description of this command? Or another command that does what longbond used to do? 
> Cheers
> Oli




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