Dear all, I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion. To verify, I chose a refinement strategy including "Anomalous groups". This worked well in an important way - R values down by 2 percentage points - but the refined f' and f" values are way off. I start out with these parameters in *.eff: anomalous_scatterers { group { selection = (name SD or name SG) f_prime = 0.319342 f_double_prime = 0.557592 refine = *f_prime *f_double_prime } group { selection = name K f_prime = 0.365562 f_double_prime = 1.06736 refine = *f_prime *f_double_prime } } What I get back is: Anomalous scatterer group: Selection: "(name SD or name SG)" Number of selected scatterers: 15 f_prime: -1.15797 f_double_prime: 0.00577091 refine: f_prime f_double_prime Anomalous scatterer group: Selection: "name K" Number of selected scatterers: 1 f_prime: -4.41689 f_double_prime: 0.00271946 refine: f_prime f_double_prime I thought I'd get close to the book values for S and would be able to identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
On Mon, Sep 8, 2014 at 12:22 AM, Andreas Förster
I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion.
You could try the ion identification feature: place_ions=K wavelength=1.54 I thought I'd get close to the book values for S and would be able to
identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity?
Naiveté, I guess. It's definitely not as accurate as Phaser's refinement of f'', for reasons that are beyond my understanding. Part of the problem is the correlation with occupancy and B-factor - especially f', which will tend to soak up any errors in occupancy and/or scattering power. -Nat
participants (2)
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Andreas Förster
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Nathaniel Echols