On Thu, Apr 4, 2013 at 12:10 PM, Francis E Reyes wrote: Does phenix.refine substitute the wavelength dependent f'/f'' when
computing f for atoms in refinement? No - I added a wavelength parameter a couple of months ago, but that is
used for ion picking, it doesn't change the input model. (Although some of
us think that might be a good idea.) phenix.maps and
phenix.find_peaks_holes *do* use the wavelength parameter in this way,
however.
(maybe it was read from a properly formatted mtz)
MTZ files always contain a wavelength - the problem is that we can't be
sure whether this was set correctly or not. I suspect that MTZ files
produced by CCP4 processing tools will have the correct wavelength, but the
downstream programs may choose to ignore this. (Most of our tools default
to writing a wavelength of 1.0; I've started to fix this but it's going to
take a while.) Or does it assume CuKa scattering factors? No, in phenix.refine atoms never become anomalous unless you specify the
anomalous groups.
-Nat