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Hi Dale, <br>
<br>
your points are all very good!<br>
<br>
Let's have a look at this at a different angle though. Bulk-solvent
is part of the model: it is the model for the other "half" of the
unit cell volume that is not interpreted in terms of individual
atoms.� <br>
<br>
If ligand is not built yet this means the program will use an
incorrect model (bulk-solvent) to describe ligand's region. Isn't it
introducing a bias?! I would think so.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/15/14 11:41 AM, Nathaniel Echols
wrote:<br>
</div>
<blockquote
cite="mid:CALeAa1Pxzya4PTN6tqoempRiCQiYZi-cS7gJQPueoy-3_JaoSA@mail.gmail.com"
type="cite">
<div dir="ltr">On Mon, Sep 15, 2014 at 8:58 AM, Dale Tronrud <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:detBB@daletronrud.com" target="_blank">detBB@daletronrud.com</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">� �An
alternative you might want to consider is what I call the<br>
"discovery map".� At some point in the refinement process
there was a<br>
map that convinced YOU that this ligand was present.� You
should be<br>
the hardest person to be convinced so that map will be
both an omit<br>
map (because the model had been refined without the ligand
prior to<br>
this) and clear enough to satisfy the reader.<br>
</blockquote>
<div><br>
</div>
<div>Agreed - this is much easier than placing the ligand
and then having to run SA. �I suspect this is a case where
"oral tradition" has been misinterpreted, since everyone
is told that the SA omit map is the "standard" for showing
unbiased difference density, and they don't realize that
it's better to simply avoid the bias to begin with.</div>
<div><br>
</div>
<div>-Nat</div>
</div>
</div>
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<br>
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