[phenixbb] phenix.composite_omit_map

Pavel Afonine pafonine at lbl.gov
Thu Feb 9 15:29:01 PST 2017

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:


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 
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,

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?

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