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On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski <[log in to unmask]>wrote: > CNS defaults to excluding them. As for phenix, I am not entirely sure - > it seems that phenix.refine does too (fill_missing_f_obs= False), but if > you use the GUI then the fill in option is turned on. In practice, it will be turned on for command-line phenix.refine too if you don't supply your own custom map definitions - actually it produces both "filled" and "unfilled" maps, but the former is what most users will see in Coot. -Nat