The rmsd command evaluates the root-mean-square deviation (RMSD) between specified sets of atoms. It differs from match in that no least-squares fit is performed (no model is moved). Atom-spec1 and atom-spec2 should contain equal numbers of atoms from two different models, respectively. The atoms need not be connected. Atoms are paired according to the order in which they are specified, i.e., the first atom of the first model is paired with the first atom of the second model, the second atom to the second atom, and so on.
If atom order is not specified, for example,
rmsd #1:fad #0:fadthe atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number.
rmsd #2:246,295 #0:195,221
All of the atoms (from both models) can be specified collectively using the word selected, sel, or picked if the current selection contains equal numbers of atoms from each model. The atoms should have been selected (most likely picked) in the proper order, first the desired atoms from one model, then the corresponding atoms in the corresponding order from the other model. When order information is lacking (for example, the atoms were selected simultaneously), the measurement may not be the one intended.
See also: match, matchmaker, measure rotation, Match -> Align, Ensemble Match, MD Movie (see RMSD analysis), superimposing structures