The peak is directly over the WO4 molecule, overlaying pretty well with the 2Fo-Fc density.<br><br>In my refinement, I refined the B-factor.<br>I will try to refine occupancy. That makes sense. If that atom is only there 50% of the time, there would be 50% less contribution, and thus I would see the negative density.<br>
<br>Thanks for the suggestions!<br><br clear="all">*******************************************************<br>Kelly Daughtry<br>PhD Candidate<br>Department of Physiology and Biophysics<br>Boston University School of Medicine<br>
590 Commonwealth Ave<br>R 390<br>Boston MA, 02215<br>(P) 617-358-5548<br>*******************************************************<br>
<br><br><div class="gmail_quote">On Thu, Apr 22, 2010 at 10:50 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
Hi Kelly,<br>
<br>
- where is the peak: at atomic center, near it and looks like a bunch
of concentric spheres? Then it might be a results of Fourier truncation
ripples; check this out where I reply to a similar post:<br>
<br>
<a href="http://proteincrystallography.org/ccp4bb/message14290.html" target="_blank">http://proteincrystallography.org/ccp4bb/message14290.html</a><br>
<br>
- did you try to refined f' and f'' of your heavy atom? Actually, I see
you did (looking at .log file);<br>
<br>
- did you try to refine its occupancy and anisotropic ADP?<br>
<br>
If you send me (to my email address, not to the whole phenixbb) the
data and model files, as well as the parameter file and exact command
you used, I will have a look.<br><font color="#888888">
<br>
Pavel.</font><div><div></div><div class="h5"><br>
<br>
<br>
On 4/22/10 6:38 AM, Kelly Daughtry wrote:
</div></div><blockquote type="cite"><div><div></div><div class="h5">Hello all,
<div>I have just used phenix autosol and autobuild to phase and build
an�initial�model of my structure with phase information from Tungsten
(W), collected at the peak wavelength of 1.2134 Angstroms.</div>
<div>Autosol works beautifully! I was able to perform W-SAD and get
great maps, when I initially thought I would have to perform W-MAD!</div>
<div><br>
</div>
<div>The problem I am having is during phenix.refine.</div>
<div>When I run the refinement (with and without refining the group
anomalous) and including my experimental phases, I see a giant negative
peak in the Fo-Fc map at the location of my Tungsten. The rest of the
map is beautiful. <br>
In the log file, I can tell that the scattering factor is high for
tungsten (see below).<br>
<br>
I believe the negative density is telling me I have too many electrons
present at the tungsten site.<br>
<br>
Can anyone help me figure out what I am doing wrong? <br>
I have attached my latest log file.<br>
</div>
<div><br>
</div>
<div>�----------X-ray scattering dictionary----------��������������� <br>
<br>
Number of scattering types: 7<br>
� Type Number��� sf(0)�� Gaussians<br>
�� W������ 1���� 73.70������ 2<br>
�� Se����� 1���� 33.92������ 2<br>
�� S����� 11���� 15.96������ 2<br>
�� Mg����� 1���� 11.95������ 2<br>
�� O���� 462����� 7.97������ 2<br>
�� N���� 343����� 6.97������ 2<br>
�� C��� 1326����� 5.97������ 2<br>
� sf(0) = scattering factor at diffraction angle 0.<br>
<br>
========================== Anomalous scatterer groups
=========================<br>
<br>
Anomalous scatterer group:<br>
� Selection: "name W"<br>
� Number of selected scatterers: 1<br>
� f_prime:������� 16.87<br>
� f_double_prime: 17.72<br>
� refine: f_double_prime<br>
<br>
Total number of atoms in anomalous groups: 1<br>
<br clear="all">
*******************************************************<br>
Kelly Daughtry<br>
PhD Candidate<br>
Department of Physiology and Biophysics<br>
Boston University School of Medicine<br>
590 Commonwealth Ave<br>
R 390<br>
Boston MA, 02215<br>
(P) 617-358-5548<br>
*******************************************************<br>
</div>
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