[Chimera-users] Visualize chain break in Chimera

[Elaine Meng]

Dear Yu Zou,
The PDB file does not explicitly say there is a chain break (there is no TER line) and there are no missing backbone atoms, so Chimera assumes that the consecutive residues in the same chain are bonded as normal.  In other structures where there are missing residues, Chimera does show the dotted line (e.g. PDB structure 1maz).

However, the bond between 127 and 128 is abnormally long (2.1 Angstroms).  Probably Pymol detects the abnormally long bond and automatically makes it a chain break.

I could tell that by hiding the ribbons (command: ~ribbon) and showing atoms (command: display) in Chimera, and then putting the cursor over the bond to show the pop-up with the bond length.  You can remove the bond, e.g. command:

~bond :127 at c:128 at n

However, it still won't show the dotted line automatically because none of the atoms are missing.  You could draw a dotted line by measuring the distance and then hiding the distance label, command:

distance :127 at c:128 at n

... and then menu: Tools... Structure Analysis... Distance, and use settings in that dialog to hide label, change color of dotted line, etc.  See attached image.

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 22, 2021, at 9:05 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation. 
> 
> This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet. 
> 
> Is there a way to visualize such chain break in Chimera?
> 
> Thanks,
> 
> Yu Zhou
> 
> 
> 
> <Pymol_chain break.jpg><Chimera_no chain break.jpg><3gbn_Ab.pdb>_______________________________________________
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