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Kelly<br>
<br>
Another thing you could try, in addition to Pavel's suggestions, is the
charge on the metal ion. Tungsten usually has a +6 charge so you can
tell phenix.refine by adding the charge in column 79-80.<br>
<br>
Nigel<br>
<br>
<tt>12345678901234567890123456789012345678901234567890123456789012345678901234567890<br>
</tt><tt>ATOM 1484 W W A 1 31.811 33.879 20.795 0.35
51.84 W+6</tt><br>
<br>
<br>
On 4/22/10 6:38 AM, Kelly Daughtry wrote:
<blockquote
cite="mid:k2j480329b21004220638v8cec2c28k964614364f570cb7@mail.gmail.com"
type="cite">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>
<pre wrap="">
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Fax : 510-486-5909 Web : CCI.LBL.gov</pre>
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