<div dir="ltr">Thanks, all. It did clear my thought. Because I always wondering why the LLG map is getting more different from the anomalous difference map and getting close to the 2FoFc map, while the anomalous difference map is almost the same as the beginning when I have no ligand put in the model.<div><br></div><div>Charles</div></div><div class="gmail_extra"><br><div class="gmail_quote">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><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 class="HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
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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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