Thanks, Pavel, for the quick feedback! Best, Nicolas ________________________________ From: Pavel Afonine Sent: Wednesday, April 8, 2020 5:31 PM To: Coudray, Nicolas; [email protected] Subject: Re: [phenixbb] refinement of EM models with hydrogens using phenix.real_space_refine [EXTERNAL] 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