[Chimera-users] display of improper peptide bond

Eric Pettersen pett at cgl.ucsf.edu
Wed Dec 18 11:06:38 PST 2013


If you look at the sequence for that chain you can see there is a 34-residue segment missing between residues 570 and 571, which is confirmed in the PDB file REMARK records with:

REMARK 400  ALL CHAINS ARE AUTOCATALYTICALLY CLEAVED BETWEEN RESIDUES
REMARK 400  570 AND 571

I guess I find it surprising that they decided to keep the numbering consecutive instead of numbering to account for the missing residues (or possibly changing chain IDs), but that's why Chimera shows a regular bond between those residues instead of a "missing structure" dashed line, and therefore why the ribbon tries to connect the residues.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Dec 18, 2013, at 9:16 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> 
> Best,
> Elaine
> -----
> 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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