On Wed, Sep 3, 2014 at 8:33 AM, PC
I see in 2y78.mtz (example I used below) has both in the MTZ:
F(+),SIGF(+),F(-),SIGF(-) I(+),SIGI(+),I(-),SIGI(-)
I am confused, why? One is sufficient isn't it?
"Why" is "because that's what the crystallographer submitted to the PDB". It's actually better to have both arrays: the intensities are (usually) the original data as measured on the detector, while the amplitudes have been processed such that negative intensities are either removed (in older versions of Phenix) or adjusted based on the French-Wilson protocol (in newer versions, and also in CCP4 utilities), and therefore do not exactly capture the original data. But the amplitudes are what the model was actually refined against, so to have a complete record of the experiment, it's helpful to have them too. (You're correct, however, that to just re-run phenix.refine we only need one of these. Note that since the original structure was refined with an older version, they may have used fewer reflections because the negative intensities were discarded.) -Nat