[phenixbb] Cadmium missing atoms

[George Phillips]

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:

> 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:
> 
> http://proteincrystallography.org/ccp4bb/message14290.html
> 
> Pavel.
> 
> 
> On 3/31/10 11:04 AM, Kristin Sutton wrote:
>> 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: ksutton at hwi.buffalo.edu
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>  
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb