Now from what you are saying I understand that there is some possibility to get into using non-truncated data with phenix? And not only that, it seems to be the default?
You make it sound like it is a bad thing. The effect of restraint weights (ADP, geometry) has most likely a much bigger impact on the final structure then a small fraction of smallish intensities (*) The French and Wilson procedure does circumvent issues with negative intensities, but depends on some prior knowledge of the intensity distribution and uses this to estimate the 'error free amplitude'. It all sounds nice, but it is not without trouble. If one has pseudo translational symmetry for instance, the basic wilson prior isn't valid. I agree at that smallish intensities are useful (if not essential in that case, depending on the degree of the PTS), but a bayesian update with an incorrect prior might even be worse. Also, why limit oneself to updating negative intensities? This is a fairly arbitrary decision rule. Also, how does one update? Do we update to the most likely posterior intensity or to the most likely posterior amplitude? These need not be the same. I fully agree with Pavel that a solution should be pursued and I also agree that the effort/payoff ratio should be used for ranking purposes. There is a intensity massaging option available in phenix, it is not default, well hidden and not for the faint of heart for reason stated above. Cheers, Peter (*): when the fraction is not small, but fairly sizeable due to pseudo translational symmetry, I definitely wouldn't want to have a French and Wilson procedure let loose on my intensities, but an ML intensity target that can deal with this kind of data is the only solution.
I suspect that French&Wilson statistics is actually applied by phenix internally if the supplied mtz-file only has intensities. If that is not the case, the problem is more serious than I thought. Otherwise it would take deliberate user effort to get into trouble, since TRUNCATE=YES is the default of the corresponding CCP4 program.
Ed.
-- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
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