The rmsd command measures the root-mean-square deviation (RMSD) between two sets of atoms in their current positions, without performing any fitting. The value is reported in the Log. The two sets must contain the same number of atoms, which will be paired in the order given. If the order is not given explicitly, chains within a model are sorted by ID, residues with a chain sorted by number, and atoms within a residue sorted by name before pairing.
To calculate RMSDs from least-squares fitting, see the align command. See also: matchmaker, measurements