I have very anisotropic data. I used the staraniso webserver to analyse and process my data which creates a final merged file with very incomplete data in the outer shells. If I use this data file in Phenix, what will happen? Will Phenix automatically fill in the unobserved data? If so, can I prevent it from doing so? I am importing the data with the reflection file editor and it seems the reflections are being filled in already at this stage.

depends on what program you use. phenix.refine always creates two sets of 2mFo-DFc maps in output mtz file. One using original data and one using missing reflections filled in with predicted values. If data set is severely incomplete you better off being careful and inspecting both maps. phenix.maps will also compute two 2mFo-DFc maps. Refinement will use original data as supplied for refinement. Pavel