The match command uses least-squares fitting 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. At least three pairs of atoms are needed to define a unique transformation, although fewer pairs can be used.
If atom order is not specified, for example,
match #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.
match #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 match may not be the one intended.
The iterate keyword indicates that successive rounds of matching should be performed. In each cycle, atom pairs are removed from the match list and the remaining pairs are fitted, until no matched pair is more than cutoff angstroms apart. The atom pairs removed are either the 10% farthest apart of all pairs or the 50% farthest apart of all pairs exceeding the cutoff, whichever is the lesser number of pairs. This excludes conformationally dissimilar regions from the final fit and allows the best-matching regions to be well superimposed.
The final root-mean-square deviation (RMSD) of just the paired atoms is reported in the status line and Reply Log. The showMatrix option (synonym show, default false) indicates whether the transformation matrix should also be reported in the Reply Log. The related command rmsd calculates an RMSD of atoms in their current positions, without any fitting.
The move option (default true) indicates whether the transformation should be performed. If false, the first model will not be moved to overlay the second, but the reported RMSD and matrix values will still reflect what would have been obtained if the transformation had taken place.
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.
See also: matchmaker, rmsd, measure rotation, matrixcopy, superimposing structures