<div dir="ltr">I have a similar question about this. when the anomalous difference map identify possible sites for Br(in my case), I should also expect to see the difference map peak at this site. If not, could this "Br" be something else?<div><br></div><div>Thanks!</div><div><br></div><div>Charles</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 9, 2014 at 11:40 AM, CPMAS Chen <span dir="ltr"><<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</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">Hi, All<div><br></div><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><br></div><div>Thanks!</div><div><br></div><div>Charles </div></div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Mon, Sep 8, 2014 at 1:23 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br></span><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr">On Mon, Sep 8, 2014 at 9:58 AM, CPMAS Chen <span dir="ltr"><<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>></span>
wrote:<br>
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<div>A difference map is used to identify whether there
is anything not-modeled, say some ligands, ions. Then
when I generate anomalous difference map, I should not
put the ligand(which contains Br) in the model, right?
Or in phenix, after I put the Br-ligand in the model,
I should not see the anomalous difference density at
the site, right?</div>
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<div>An "anomalous difference map" is a map of the anomalous
differences DANO (Fobs(+) - Fobs(-)). It's independent of
Fcalc, so it doesn't matter if you put the ligand in or
not. <br>
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This is not quite an accurate statement. To calculate a Fourier map
one requires amplitudes and phases. (Fobs(+) - Fobs(-)) are the
amplitudes for the anomalous difference map. The phases come from
Fcalc (actually from Fmodel), one way or another.<span><font color="#888888"><br>
<br>
Pavel<br>
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</blockquote></div></div></div><br><br clear="all"><span class=""><div><br></div>-- <br>
<p></p><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><p></p>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>
<p></p><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><p></p>
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