Hi! If I understand the question correctly, in the GUI you can use the tool "Superpose maps" in the maps tab. It takes 2 models and their associated maps and superimposes them. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] Sent: Thursday, July 16, 2015 11:19 AM To: Mullins, Elwood A.; PHENIX user mailing list Subject: Re: [phenixbb] Map alignment Is it possible to align two structures and two maps without moving both to a P1 box? No, I don't think it is possible. Pavel