Hi, I have two cryo-EM models (PDBs) at neutral and acidic pH conditions, both containing 486 amino acids. I would like to compare them by calculating the RMSD per residue, and then generate a morphing animation between the two structures. I used the following commands in ChimeraX: 1. I aligned the two structures using MatchMaker: mm #1 to #2 showAlignment true 2. I clicked on one amino acid in the MatchMaker alignment results to highlight the aligned residues. 3. Then I used the command: select ~sel to select residues with an RMSD greater than 1 Å. 4. To visualize the atoms of the selected residues with high RMSD, I ran: display sel & protein 5. I then cleared the selection using: select clear 6. Finally, I attempted to generate a morphing animation using: morph #1,2 wrap true frames 60 However, this command did not work. Could you please help me troubleshoot this? Thank you. Kind regards, Priyanka