[phenixbb] refinement of EM models with hydrogens using phenix.real_space_refine

[Pavel Afonine]

Hi Nicolas,

>    We had a question regarding how the phenix.real_space_refine works 
> when used to refine CryoEM models with hydrogens: are hydrogens 
> treated as riding or are they explicitly refined?

yes, they are riding (although the way real-space refinement work in 
phenix.real_space_refine it doesn't matter!).
Also, they are not included into map target function calculation.

Pavel

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