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<p>Thanks, Pavel, for the quick feedback!</p>
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<p>Best,</p>
<p>Nicolas<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Wednesday, April 8, 2020 5:31 PM<br>
<b>To:</b> Coudray, Nicolas; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] refinement of EM models with hydrogens using phenix.real_space_refine</font>
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<p><span style="color:#ff0000"><strong>[EXTERNAL]</strong></span></p>
<div>Hi Nicolas,<br>
<br>
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<div id="divtagdefaultwrapper" dir="ltr" style=""> We had a question regarding how the
<span>phenix.real_space_refine</span> works when used to refine CryoEM models with hydrogens: are hydrogens treated as riding or are they explicitly refined? </div>
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yes, they are riding (although the way real-space refinement work in phenix.real_space_refine it doesn't matter!).<br>
Also, they are not included into map target function calculation.<br>
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Pavel<br>
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