Thanks Pavel but it only takes mtz as input. I'm also only interested in the transformation matrix to suppose one map onto the other in their original frame of reference without superposing the maps per se.

On Sun, Dec 20, 2020, 2:19 PM Pavel Afonine <pafonine@lbl.gov> wrote:

Hi Ahmad,
phenix.match_maps is the tool to superpose maps and models.
Pavel

On Sun, Dec 20, 2020, 1:38 PM Ahmad Khalifa <underoath006@gmail.com> wrote:
I have two density maps that I'm trying to align, or more precisely, calculate the transformation matrix (rotation and translation) of their alignment (moving one map and aligning it with the other map). Is there a way to accomplish that using phenix or any other tool?

Thanks a lot and happy holidays.
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