Hi Fred, by default phenix.composite_omit_map does not do any refinement (omit_type=simple) and it computes composite OMIT map as described in Figure 6 here: http://journals.iucr.org/d/issues/2015/03/00/lv5075/lv5075.pdf Optionally, you can ask it to do refinement with (omit_type=anneal) or without (omit_type=simple) Simulated annealing. You don't have control over refinement that happens in phenix.composite_omit_map. I don't think it's important though.. The goal of running phenix.composite_omit_map is not to get the best refined model but to answer questions that OMIT map is helpful at. I doubt that imperfect geometry of secondary structure that may come out of refinement without specific restraints is going to impact the utility of OMIT map. All the best, Pavel On 2/7/17 13:03, Dyda wrote:

I have a moderate resolution structure that I refined using secondary structure restraints (both for nucleic acid and for protein)

I'd like to use phenix.composite_omit_map to calculate such a map.

Is it possible (and if so how) to make phenix.composite_omit_map to use the same restraints during annealing of the not omitted parts?