Hi,

I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. 

These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful

As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows:

Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native)

The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps ->  Make a difference map"

There were two things I was unsure about:

Does this seem like a reasonable alternative? 

Is scaling of the two datasets required before generating the difference map?

Cheers, 

Jordan