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: [email protected]
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