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<p>Hi,</p>
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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://phenix-online.org/documentation/reference/real_space_refine.html" class="OWAAutoLink" id="LPlnk565308" previewremoved="true">
https://phenix-online.org/documentation/reference/real_space_refine.html</a>):</p>
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<ul>
<li class="phil-param" data-expert="0"><span class="phil-name">hydrogens</span><span class="phil-words"> = False
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">main_chain</span><span class="phil-words"> = True
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">side_chain</span><span class="phil-words"> = True
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">fix_outliers</span><span class="phil-words"> = True
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">strict_rotamer_matching</span><span class="phil-words"> = False
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">auto_shutoff_for_ncs</span><span class="phil-words"> = False
</span></li><li class="phil-param" data-expert="0"><span class="phil-name">secondary_structure_only</span><span class="phil-words"> = False
</span></li></ul>
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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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</p>
<p>Thanks,</p>
<p>Best,</p>
<p>Nicolas</p>
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