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Hi Ezequiel,<br>
<br>
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">I added a
Cu(II) ion in a blob of density using Coot (this metal is used
in crystallization solution). When I refined using phenix, I
noted that occupancy does not change from the arbitrary value
that I set in Coot, </div>
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<br>
if this value greater than zero and less then one, and you did
enable occupancy refinement, then the occupancy should be refined.
Is that what you did and still get occupancy unrefined?<br>
<br>
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">and negative
density remains when refinement is complete. </div>
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<br>
Not surprisingly if occupancy was not refined. So please make sure
you do refine occupancy.<br>
<br>
<blockquote
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">When I
manually adjust occupancy to 0.3, </div>
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<br>
No need to do so as phenix.refine will normally refine it.<br>
<br>
<blockquote
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">phenix
changes it to 0.29, </div>
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<br>
Ok, well, this contradicts to what you wrote above: occupancy does
change during refinement.<br>
<br>
<blockquote
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<div style="color:#000; background-color:#fff;
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">and no
negative density is seen, however B-factor does not move from
my arbitrary setting of 30 in Coot. I worry if something is
wrong in my refinement strategy. I thank any suggestion.</div>
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<br>
Do you refine it?<br>
<br>
<blockquote
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<div id="yui_3_16_0_1_1437956031803_5593" dir="ltr">Some
additional information: my mtz is merged F's, resolution is
1.3 A, refinement strategy includes XYZ coordinates,
Occupancies and Individual B-factors.<br>
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<br>
No need to ask this as it is obvious, but just on case: you do
refine anisotropic ADPs at this resolution, correct?<br>
<br>
This may be worthwhile checking:<br>
<br>
- Occupancy and ADP refinement sections of phenix.refine
documentation:<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/documentation/reference/refinement.html">https://www.phenix-online.org/documentation/reference/refinement.html</a><br>
<br>
- Pages 8-14 here:<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/presentations/faq.pdf">https://www.phenix-online.org/presentations/faq.pdf</a><br>
<br>
If you are still having troubles or questions please let me know. I
may need input data and model files to investigate further.<br>
<br>
Pavel<br>
<br>
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