<div dir="ltr">Hi Pavel,<div><br></div><div>The B-factors of these atoms are quite high (most are 100+), so maybe the occupancy is compensating as you said. After refinement, the maps don't look much different. Perhaps it's not worth bothering with occupancy refinement, then?</div><div><br></div><div>I think you got my question. I was asking if it is unusual that only 5/93 occupancies were refined to values other than 0 or 1.</div><div><br></div><div>Best,</div><div>Chris</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 5, 2016 at 6:38 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Chris,<span class=""><br>
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I've built several glucose molecules from my cryosolution into regions of weaker electron density. Attempting to refine the occupancies of the corresponding atoms, I set the value of each to 0.25 in the pdb file. However, after running phenix.refine, most of the atoms still have occupancies of 1.00:<br>
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perhaps they are fully occupied but highly mobile which explains weak density? Or B-factor refines to larger value so that occupancy tries to compensate? How maps look like after refinement?<span class=""><br>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
14 atoms with occ = 0.00<br>
5 atoms with 0.00 < occ < 1.00<br>
74 atoms with occ = 1.00<br>
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Is this unusual?<br>
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Do you mean is it unusual to have 5 atoms in your structure with occupancies between 0 and 1? Hm.. I don't know, may be not! I think I'm not understanding what's the real question here..<span class="HOEnZb"><font color="#888888"><br>
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Pavel<br>
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