I am very lucky to see 2 maps of the same protein, at roughly the same resolution, one by Xray and the other by EM (it's not that common). The details from the 2 maps are however different...

Here is my procedure, please let me know what you think:
- convert .mrc map to .mtz ; I get F, PHIF.
- supperpose the maps:
map1: labels 2FOFCWT, PH2FOFCWT
map2: F, PHIF.
I also provided the 2 PDBs as it is clearly stated on the input files definitions.

It worked, with the 2 maps superposed that I can look and compare.

However, for some reason, the superposition has been done on chain C and D of the crystallograhic model instead of chain AB (4 chains in the asymmetric unit, making 2 dimers). Is there a reason there, choosing the closest structure, best fit? (I see that it is possible to define a superposition)

Another thing is that it creates a "supperposition in the middle", meaning neither on model1 nor model2 from the input, and not a crystallographic symmetric of model1. So I can't use the full crystallographic maps, I have a "simplified" version of it.