<div dir="ltr"><div><div><div><div>Thank you guys so much for your suggestions! <br></div>Yes, I think it's true that "if ligand density is
strong enough it may not be masked by the bulk-solvent completely". In my case, <br>I have two different ligands in the protein-ligand structure, and using the method I described in the first email, one of the ligand has good, continuous green density but for the other ligand, <font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none">as I described before, contoured at 2<span>σ</span>,
the Fo-Fc map generated show green density for most part of the ligand,
but for several atoms in the middle of the ligand, the green density is
missing...<br></span></span></font></div><br></div>Hi Nat, you mentioned that <br></div><div><div>1. "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."<br></div><div><br>I am wondering how this could be done. <br><br></div><div>2. "Restraining
the zero-occupancy ligand (and perhaps adjacent residues) is strongly
recommended, especially if it contains heavier elements. (The newer
versions of the phenix.refine GUI have a button in the Output tab to set
this up.) Without restraints, you run the risk of refining the
surrounding model into the ligand density. As always this is worse at
lower resolution - at 2.8Å I'm not sure what to expect."<br><br></div><div>I am wondering how this could be done. <br></div><div><br></div>Thank you guys so much!<br><br>Best, <br>Wei <br></div><div><div><br><br><br><br><div><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none"><br><br><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none"></span></span></font></span></span></font></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Sep 13, 2014 at 9:13 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">
<div bgcolor="#FFFFFF" text="#000000"><span class="">
<br>
<div>On 9/13/14 5:57 PM, Nathaniel Echols
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Sat, Sep 13, 2014 at 3:03 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<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>
</div>
</blockquote>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<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>
</div>
</blockquote>
<div><br>
</div>
<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>
</div>
</div>
</div>
</blockquote>
<br></span>
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><span class="HOEnZb"><font color="#888888">
<br>
Pavel<br>
<br>
</font></span></div>
</blockquote></div><br></div>