[phenixbb] refinement of EM models with hydrogens using phenix.real_space_refine
Nicolas.Coudray at nyulangone.org
Wed Apr 8 15:44:22 PDT 2020
Thanks, Pavel, for the quick feedback!
From: Pavel Afonine <pafonine at lbl.gov>
Sent: Wednesday, April 8, 2020 5:31 PM
To: Coudray, Nicolas; phenixbb at phenix-online.org
Subject: Re: [phenixbb] refinement of EM models with hydrogens using phenix.real_space_refine
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.
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