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 are matched 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, second atom to second atom, etc. The command syntax allows much flexibility in specification, that is, atom specifications can use all the shorthand available for related atoms. For example, the user might match models 1 and 2 thus:
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. Specifying the active option will make match transform not only the first model mentioned in the command line but also any other models that are activated for motion (except the second model mentioned in the command line), using the same transformation that was applied to the first model.
The user should be aware that the order in which atoms are specified in a list does not necessarily force the order in the match. For example,
match #1:3@C1,C2,P,O2 #2:3@C1,C2,P,O2is not specific as to the order of the atoms C1, C2, P and O2. In this case, the atoms will be ordered as they occur in the residue connectivity for residue 3. If residue 3 of model 1 and residue 3 of model 2 are the same, this is not a concern. If they are different, however, then the order is not specific and the models may not be superimposed as expected. Ordering may be forced by using the @ designation, as in the first example.
The RMSD value from the least squares fit is returned in the command reply area. The value is only for those atoms named in the match command (since the models being matched may or may not have identical numbers of atoms).