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]
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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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: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
George Phillips -
Kristin Sutton -
Pavel Afonine