This app computes the root mean square deviation (RMSD) in Angstrom between two PDB-format structures. It is important to note that both PDB files must have an identical number of atoms for the script to function properly. The RMSD quantifies the average distance between corresponding atoms in two protein or ligand structures using the RMSD equation. Typically, RMSD calculations exclude hydrogen atoms, focusing on C-alpha or main-chain atoms in proteins.

Both structures must contain the same number of atoms in similar order.

Based on the GitHub: https://github.com/rasbt/protein-science?tab=readme-ov-file#substructure-alignment-using-openeye-oechem-rmsd

Try out with this data: https://github.com/rasbt/protein-science/tree/master/scripts-and-tools/rmsd/data