How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"?

Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment."

How should I compare two chromosome 3D models below? Thank you.

Best regards,

Zichen "Cardiff" Jiang