Hi Appu, at such low resolution you need to use as much information as possible, such as secondary structure restraints. There is no sufficient information in the data alone to preserve secondary structure. It is not surprising it deteriorates after SA. Using Maps->Composite omit map with all defaults should be fine in most cases. Pavel On 2/29/16 06:47, Appu kumar wrote:

Hello All, I am trying to make the simulated annealing composite omit map for a protein ligand complex at 4.37A resolution. I think, Simulated annealing is harsh and rendering the protein distorting a lot as is evident from the helix turning into the some random structure. In order to avoid this protein distortion in protein backbone, do I need to fix some weight or specific parameter or provide reference structure and put harsh weight ? Any advice or suggestions would be much appreciated. Appu