The rmsd command evaluates the root-mean-square deviation (RMSD) between specified sets of atoms, without any fitting. The related command match performs least-squares fitting. See also: superimposing structures
Atom-spec1 and atom-spec2 must specify equal numbers of atoms.
Atoms are paired in the order specified, i.e., the first atom in the first specification is matched to the first atom in the second specification, 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
The two sets of atoms can be specified collectively as a selection using the word selected, sel, or picked. An ordered selection can be created by picking atoms one by one, first the atoms of the first set, then those of the second in the corresponding order.