On Wed, May 29, 2013 at 4:18 AM, Derek Logan
What's going on here? If I let phenix.refine decide automatically, it looks like it's reading in F+ and F- separately and regarding them as independent in the refinement. If I force "no anomalous" it merges them. However I can't work out whether in either case it has actually read FOBS instead of the Friedel mates.
Technically it's reading the merged amplitudes plus the anomalous differences*, and reconstructing the original Friedel pairs from these, hence "reconstructed amplitudes". We generally recommend just using the actual F+/F- (or I+/I-) instead of the reconstructed arrays, but if you have the ISYM column it probably doesn't matter too much. (And I realize that for neutron diffraction it's pointless either way, but we try not to assume too much about what the user wants.) (* By the way, does anyone actually understand why CCP4 programs outputs DANO,SIGDANO as separate columns? What programs actually use this in preference to the Friedel pairs?)
According to the SCALA manual the I+ and I- columns will always be written out even if the keyword ANOMALOUS OFF is used, so this is a potential pitfall for many.
I will add a warning to the GUI about this.
In addition, phenix.refine seems to identify the neutron data first as xray.reconstructed_amplitude then as xray.amplitude even though the data are explicitly defined as neutron data in the GUI.
That's an implementation detail - Ralf wrote all of the code to handle experimental observations with the assumption that it would be X-ray data, which (at least) 99% of the time would be true. It won't actually make any difference to the way scattering is treated as long as you select the neutron scattering table. But perhaps we should add a disclaimer to the log output... -Nat