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@cgl.ucsf.edu> wrote:
Hi Tatiana, You could delete the bond with a command, e.g.
~bond :570@c :571@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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