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<p>Hi Oleg - <br>
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<p>Thanks a lot for the detailed answer!</p>
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<p>Best,</p>
Nicolas</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Oleg Sobolev <osobolev@lbl.gov><br>
<b>Sent:</b> Monday, November 8, 2021 5:34 PM<br>
<b>To:</b> Coudray, Nicolas<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Parameters in "reference_model" during "real space refinement"</font>
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<p><span style="color:rgb(209,72,65)"><span style="font-family:"Times New Roman",Times,serif; font-size:22px"><strong>[EXTERNAL]</strong></span></span></p>
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<div dir="ltr">Hi Nicolas,
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<p> I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in
<a href="https://urldefense.com/v3/__https://phenix-online.org/documentation/reference/real_space_refine.html__;!!MXfaZl3l!PtWqAe3o6W8tEknDNzye9dt1zcMId4s7Fwi7FlTHKnwm_LpnuvvbbT43oWcVljUKnzq_q53I$" id="gmail-m_3761747893674855406LPlnk565308" target="_blank">
https://phenix-online.org/documentation/reference/real_space_refine.html</a>):</p>
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<div>Given that reference model restraints are dihedral restraints derived from reference model and applied to refined model: <br>
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<li><span>hydrogens</span><span> = False</span></li></ul>
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<div>Include dihedrals that include hydrogen atoms</div>
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<li><span>main_chain</span><span> = True</span></li></ul>
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<div>Include dihedrals formed by main chain atoms</div>
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<li><span>side_chain</span><span> = True</span></li></ul>
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<div>Include dihedrals formed by side chain atoms</div>
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<li><span>fix_outliers</span><span> = True</span></li></ul>
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<div>Try to fix rotamer outliers in refined model</div>
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<li><span>strict_rotamer_matching</span><span> = False</span> </li></ul>
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<div>Make sure that rotamers in refinement model matches those in reference model even when they are not outliers</div>
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<li><span>auto_shutoff_for_ncs</span><span> = False</span></li></ul>
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<div>Do not apply to parts of structure covered by NCS restraints</div>
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<li><span>secondary_structure_only</span><span> = False</span> </li></ul>
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<div>Only apply reference model restraints to secondary structure elements (helices and sheets)</div>
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<p>It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information?</p>
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<div>In the majority of cases default parameters should be good.</div>
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<div>The paper on this is: </div>
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. J. J. Headd, N. Echols, P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, N. W. Moriarty, D. C. Richardson, J. S. Richardson, P. D. Adams. Acta Crystallogr
D Biol Crystallogr 68, 381�390 (2012). doi:10.1107/S0907444911047834
<div><a href="https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2012/04/00/ba5171/index.html__;!!MXfaZl3l!PtWqAe3o6W8tEknDNzye9dt1zcMId4s7Fwi7FlTHKnwm_LpnuvvbbT43oWcVljUKn0vpuxn6$">https://journals.iucr.org/d/issues/2012/04/00/ba5171/index.html</a> </div>
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<div>Please let us know if you have more questions.</div>
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<div>Best regards,</div>
<div>Oleg Sobolev.</div>
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<p>Thanks,</p>
<p>Best,</p>
<p>Nicolas</p>
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