[phenixbb] Cadmium missing atoms

Pavel Afonine PAfonine at lbl.gov
Wed Mar 31 11:16:28 PDT 2010


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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