Usage:
match [ iterate cutoff ] [ active ] atom-spec1 atom-spec2

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 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 matched to the first atom of the second model, the second atom to the second atom, and so on. The first model will be transformed so that its atoms overlay those of the second model.

The match root-mean-square deviation (RMSD) in angstroms is reported in the status line and Reply Log. The RMSD calculation includes only the atoms used to match the models. The related command rmsd calculates an RMSD without performing a least-squares fit.

The iterate keyword indicates that successive rounds of matching should be performed, each round excluding atom pairs more than cutoff angstroms apart after the previous round. Matching is iterated until no atom pairs used for matching are more than cutoff angstroms apart.

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.

It is prudent to use an ordered specification, such as

match #1:3@C1@C2@P@O2 #2:3@C1@C2@P@O2

match #1:3@C1,C2,P,O2 #2:3@C1,C2,P,O2

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: matchmaker, rmsd, matrixcopy, Match -> Align