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.

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.)

 

No, in phenix.refine atoms never become anomalous unless you specify the anomalous groups.

-Nat