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<div class="moz-cite-prefix">On 9/13/14 5:57 PM, Nathaniel Echols
wrote:<br>
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cite="mid:CALeAa1NYdgL=yKeyjNLQKgyNp10fsHWiMdZ6z=BTDPP35Pizgg@mail.gmail.com"
type="cite">
<div dir="ltr">On Sat, Sep 13, 2014 at 3:03 PM, Pavel Afonine <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
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<div bgcolor="#FFFFFF" text="#000000">In the first case
the bulk-solvent mask will be set in the ligand region
and therefore it will mask ligand density (bulk-solvent
will be filled into the ligand region). Depending on the
strength of ligand density it may be masked completely
or deteriorated.<br>
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<div bgcolor="#FFFFFF" text="#000000"> If you follow the
second option you will always get positive density in
ligand area. This density may correspond to
bulk-solvent, ligand or mixture of both. That is there
will be no simple way to differentiate whether this
density arises from the ligand or bulk-solvent.<br>
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<div>I thought phenix.refine ignores zero-occupancy atoms
when calculating the bulk solvent mask? �In fact there is
an option specifically to toggle this option, and I've
noticed very different results with and without it.</div>
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It is bad both ways:<br>
� 1) If you ignore zero occupancy atoms then you fill bulk-solvent
into ligand region and therefore mask the ligand;<br>
� 2) If you do not ignore zero occupancy atoms then what you compute
is bulk-solvent-omit map in region around atoms with zero occupancy.
This means that the "green" density you are going to see may be
ligand or may be bulk-solvent or may be the mixture of the two.<br>
<br>
In fact, #1 above is better than #2 because if ligand density is
strong enough it may not be masked by the bulk-solvent completely. <br>
<br>
Pavel<br>
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