[phenixbb] Cadmium missing atoms

Pavel Afonine PAfonine at lbl.gov
Wed Mar 31 12:01:03 PDT 2010


Absolutely! Refining f' and f'' may help (if your data contains Fobs(+) 
and Fobs(-)).

Pavel.


On 3/31/10 11:52 AM, George Phillips wrote:
> 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
>>>
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>>>  
>>>       
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