As I have not been able to find basic newbee information anywhere regarding how to convert a Cryo-EM map to mtz, I will just note down what I did. I have no idea if it is the “correct”way or not, but it works.
Basically I just used the phenix program: phenix.map_to_structure_factors with my EM map (in mrc or ccp4 format, they are normally identical formats) as input together with a resolution constant (d_min) e.g.
phenix.map_to_structure_factors CrappyEMmap.mrc d_min=4.4
and out comes a mtz file for you.