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: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jason Porta [jpo...@unmc.edu] Sent: Tuesday, October 18, 2011 6:16 PM To: CCP4BB@JISCMAIL.AC.UK 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