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Hi all,</div>
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I am trying to navigate phenix.refine to occupancy refine a partially occupied inhibitor vs. the waters that it displaces.</div>
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For instance I have molecule resseq 802 in chain A, and waters 1-6 in chain W that are overlapping. When just refining occupancy of the molecule there are clear sites for the waters. How can I refine both of them together so that I can get an occupancy of
the molecule vs the group of waters (which should have nearly identical occupancies)?</div>
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Maybe, a bit more information on the differences in refinement strategy for the occupancy vs fix occupancy vs group occupancy would be more broadly helpful.</div>
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I tried to make them all a group, but that didn't work as the refinement pushed the waters out and reduced their occupancies to ~0 while leaving the small molecule occupancy about the same as without water.</div>
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<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><img size="656363" contenttype="image/png" style="max-width: 1031px;" data-outlook-trace="F:1|T:1" src="cid:2b35e3b8-08e5-44ae-9b70-8fdcff613f1a"></span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>*Waters are only placed, they are not refined), small molecule is refined to 0.71
occupancy.</b>*</span></div>
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--<br>
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<div style="direction: ltr;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><b>Matthew Jordan McLeod, PhD</b></span></div>
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<span style="font-size: 12pt; color: rgb(136, 136, 136);">Post-Doctoral Fellow |<i> </i>Thorne Lab</span></div>
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