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Hi Subhani,<br>
<br>
here is some text that I posted on a bb a while ago, so I'm
copy-pasting it with some minor updates:<br>
<br>
These could be Fourier series truncation ripples or residual density
features that are typically more pronounced for heavier atoms at
higher resolutions.<br>
Some relevant information to have a look:<br>
<br>
1) Pages 19-21, 30, 32, 33 here:<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_maps.pdf">http://www.phenix-online.org/presentations/latest/pavel_maps.pdf</a><br>
<br>
2) CCP4 Newsletter<br>
<a class="moz-txt-link-freetext" href="http://www.ccp4.ac.uk/newsletters/newsletter42/content.html">http://www.ccp4.ac.uk/newsletters/newsletter42/content.html</a><br>
On the Fourier series truncation peaks at subatomic resolution<br>
Anne Bochow, Alexandre Urzhumtsev<br>
<br>
3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at
1.16 <br>
Å Resolution: A.<br>
Oliver Einsle, et al. Science, 1696 (2002) 297<br>
<br>
4) Page 267 Figure 4:<br>
On the possibility of the observation of valence electron density
for <br>
individual bonds in proteins in conventional difference maps<br>
P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev<br>
Acta Cryst. (2004). D60, 260-274<br>
<br>
Suggestions for refinement are:<br>
<br>
1) make sure the atom is not pulled out of density by incorrectly
defined/applied restraints or their absence.<br>
2) if site may be partially occupied then try occupancy refinement;<br>
3) refine anisotropic ADP for this site;<br>
4) try f' and f'' refinement if applicable;<br>
5) try more refinement macro-cycles: achieving convergence of
refinement of occupancy/b-factor may take longer.<br>
6) if none of 1)-5) helped and you are convinced that this is
Fourier truncation effect then leave it alone.<br>
<br>
Pavel.<br>
<br>
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<br>
<br>
On 3/28/12 9:05 AM, Subhani Bandara wrote:
<blockquote
cite="mid:CAPCm4u_wUaji6stegBb0R5xNwGdEPJX1=Wy8yVfuVGHCq-aXMg@mail.gmail.com"
type="cite">Hi everyone,
<div><br>
</div>
<div>I have refined a protein with a metal-chelate complex at 1.4
resolution and saw positive density around some metals that are
on a two fold. I refined those chelator complexes with fixed
occupancy to avoid the negative density seen around it as they
are partially occupied. Also I had to avoid xyz refinement after
fixing them on special position, to avoid moving away from two
fold. I have attached a figure of one of those complexes. If I
increase occupancy then it shows negative density. How can I get
rid of this positive density.</div>
<div><br>
</div>
<div>Thanks in advance for the help</div>
<div><br>
</div>
<div>Subhani<br>
</div>
</blockquote>
<br>
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