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
