Hi Kaina and Elaine, If the goal is just to demonstrate the similarities of the two domains in your proteins, you could also consider breaking the model in two and superimposing each domain separately. Another feasible but tedious approach for rotating bonds (which I do not recommend because it means altering the structure from what was observed) would be to measure torsion angles in the protein backbone of the "linker" region of one model and then set the torsion angles into the same values in the other model, using the command line or a script. Best, -Martti -- Martti Tolvanen Lecturer in bioinformatics U of Turku, Finland -----Original Message----- From: chimera-users-request@cgl.ucsf.edu [mailto:chimera-users-request@cgl.ucsf.edu] Sent: 11. helmikuutata 2022 23:31 To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 226, Issue 6 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."