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