The match command uses the least-squares fit method to superimpose two models. Atom-spec1 and atom-spec2 should contain equal numbers of atoms from two different models, respectively. The order of specification is important, but atoms need not be connected. The match root-mean-square deviation (RMSD) in angstroms is reported in the status line and Reply Log. The RMSD value is only for the specified atoms.
The related command rmsd calculates an RMSD without performing a least-squares fit.
Atoms are paired according to the order in which they are specified, i.e., the first atom of the first model is matched to the first atom of the second model, the second atom to the second atom, and so on. For example:
match #1:3@C1@C2@P@O2 #2:3@C1@C2@P@O2
The first model will be transformed so that its atoms overlay those of the second model. If the active keyword is given, not only the first model will be transformed, but also any other models that are activated for motion (except the second, reference model), using the same transformation that was applied to the first.
Note that
match #1:3@C1,C2,P,O2 #2:3@C1,C2,P,O2does not actually specify the order of the atoms C1, C2, P and O2. Ordering can be forced using the @ designation, as in the first example.
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 match may not be the one intended.
See also: matrixcopy, rmsd