What's wrong with cis-peptides? there are plenty of those in the PDB, independent of the presence of proline. If they fit the density better and neighbouring residues are happy, just go with it. The refinement suggests that this could indeed be the case.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Jason Porta [[log in to unmask]]
Sent: Tuesday, October 18, 2011 6:16 PM
To: [log in to unmask]
Subject: [ccp4bb] Fixing cis peptides
Hi everybody,
I am currently refining a 2.2 A crystal structure with a very mobile subdomain. The initial density for this subdomain was very weak, however, I was able to rebuild it using low resolution omit maps (and some perturbing of atomic coordinates). When I refine the structure, four of the peptide bonds go into the cis position. When I fix it manually, many clashes are introduced, and even then, the structure just refines back into the cis positions.
Does anyone have a good technique for dealing with cis bonds? Or any advice on how I could fix this?
regards,
Jason P
