[Chimera-users] display of improper peptide bond

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 18 09:16:35 PST 2013

Hi Tatiana,
You could delete the bond with a command, e.g.

~bond :570 at c :571 at n

Based on the ATOM records and PDB format specifications, they would be considered as connected (consecutive standard residues with same chain ID, no TER, ...), so it should be an unusual case.  Chimera doesn't distance-test in these "standard residue" situations.

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 18, 2013, at 5:52 AM, Tatiana Domitrovic wrote:

> Hi,
> I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work. 
> Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue  570 and 571.
> Cheers,

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