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Absolutely! Refining f' and f'' may help (if your data contains Fobs(+)
and Fobs(-)).<br>
<br>
Pavel.<br>
<br>
<br>
On 3/31/10 11:52 AM, George Phillips wrote:
<blockquote
cite="mid:E3B6A68E-5AE0-4E4F-A0D6-09E15B766402@biochem.wisc.edu"
type="cite">
<pre wrap="">Or anomalous scattering effects, depending on the wavelength you used...
Occupancies will help correct for this, even if they are 100% present.
George N. Phillips, Jr., Ph.D.
Professor of Biochemistry and of
Computer Sciences
University of Wisconsin-Madison
433 Babcock Dr. Madison, Wi 53706
Phone/FAX (608) 263-6142
On Mar 31, 2010, at 1:16 PM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Kristin,
for these ions in refinement you may need to:
- make sure that the charge (if any, non-zero) is included (use the latest PHENIX for this);
- refine anisotropic ADPs;
- refine occupancies.
If you still have some surrounding residual density then that may be attributed to Fourier truncation effects:
<a class="moz-txt-link-freetext" href="http://proteincrystallography.org/ccp4bb/message14290.html">http://proteincrystallography.org/ccp4bb/message14290.html</a>
Pavel.
On 3/31/10 11:04 AM, Kristin Sutton wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello-
I am refining a structure with 2 cadmium ions present. From the extensions
menu in coot, I clicked on modeling >> residues with missing atoms, and both
Cadmium ions came up in that list. The density surrounding these atoms is
also strange, positive density right in the middle of the atom, negative
density surrounding the whole atom. How do I make sure these are being
refined correctly?
Thank you in advance,
Kristin
********************************************************************
Kristin A. Sutton
Graduate Student
University of Buffalo
Department of Structural Biology
Hauptman-Woodward Medical Research Institute
700 Ellicott Street
Buffalo, NY 14203
P: (716)898-8683
F: (716)898-8600
E: <a class="moz-txt-link-abbreviated" href="mailto:ksutton@hwi.buffalo.edu">ksutton@hwi.buffalo.edu</a>
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