[phenixbb] model shifts after real space refinement

Pavel Afonine pafonine at lbl.gov
Wed Dec 15 15:33:29 PST 2021

Hi Ashok,

a usual suggestion here: first, try latest version of Phenix (1.20-4444) 
found here:


to check if the problem still exists. Please get back to us if it does 
and we will investigate further.


On 12/15/21 07:44, Ashok Nayak wrote:
> Hi,
> Is there a way to say keep_origin=False in phenix real space 
> refinement. I used it in the command line version of v3958. It didn't 
> take that.
> There is a model shift after the refinement which I think is because 
> the program brings the map to the origin and hence the refined model 
> as well.
> Thanks,
> Ashok
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