phenix.match_maps can overlay model B and map B onto model A and map A. A and B can be any symmetry and box (unit cell) dimensions. Model A and map A stay in its original frame of reference. Let me know should you have questions.

Pavel

On 5/11/20 15:18, Murpholino Peligro wrote:

I want to compare electron density features of map A from protein A and map B from protein B...

Because each map has a different rmsd level...

...what is the best way to compare electron density between maps?

Is there a way to normalize maps or something like that?

Thanks
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