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Hi Charles,<br>
<br>
I think the key here is what you call "<span class="">no difference
density peak</span>". Sites may be partially occupied so rule of
thumb for choosing contouring levels for 2mFo-DFc and mFo-DFc maps
(1 and 3 sigma, correspondingly) may not be appropriate, for
instance.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/10/14 6:10 AM, CPMAS Chen wrote:<br>
</div>
<blockquote
cite="mid:CAAU4GKae_VtbWhtXaBrwtb1so_sxi4i_pf6zAcMiWHkxB8oMkg@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks, Nat.
<div><br>
</div>
<div>If this is noise, why the anomalous or LLG peaks could be
as high as 5 ~ 6 sigma? </div>
<div><br>
</div>
<div>Charles</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Sep 9, 2014 at 5:58 PM,
Nathaniel Echols <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:nechols@lbl.gov"
target="_blank">nechols@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 dir="ltr"><span class="">On Tue, Sep 9, 2014 at 8:40
AM, CPMAS Chen <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>></span>
wrote:<br>
</span>
<div class="gmail_extra">
<div class="gmail_quote"><span class="">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Is it possible that I have anomalous and
LLG peak, but I have no difference density
peak? In this case, is that because the model
I have is not good enough or the diffraction
data at this site of the model is missing?</div>
</div>
</blockquote>
<div><br>
</div>
</span>
<div>You should at a minimum see > 1sigma density
in the 2mFo-DFc map, and if the site is unmodeled
(or modeled as a water) you should see an mFo-DFc
peak as well. If neither of these applies, the
anomalous and LLG peaks are probably just noise.</div>
<div><br>
</div>
<div>-Nat </div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<p>***************************************************</p>
<p>Charles Chen</p>
<p>Research Associate</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************************************</p>
</div>
</blockquote>
<br>
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