I recently went through this - I had a .sca file that had gone through the Scalepack2mtz -> Truncate route, then used it in phenix, and since Imean and SigImean are still present in the MTZ file phenix.refine uses those. As per Pavel it simply converts them to F's by square root, discards Imean less than/equal to zero. This is the DEFAULT behavior, and so quite pernicious and easy to miss. I caught this while checking R-free in shells and noticed lower completeness than Scalepack indicated, as per my example. Phil
Phil,
I have always used denzo/scalepack, and then scalepack2mtz to convert .sca file to .mtz file. So my data is always processed according to French&Wilson.
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?
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.