Standard superimposition works well when the sequences of the proteins to be compared are similar and they do not display flexible domains or regions (e.g., hinges or loops). Fitting is performed using the McLachlan algorithm.
Weighted superimposition finds the better "alignable" core in both structures after perfoming a sequence alignment and establishing atomic equivalence. This method is useful when a minority of residues are different or flexible in the two proteinss. Examples include hinges, loops, tails, etc.
Structural superimposition is ideal in cases where the sequences of both proteins differ. The method finds the residue-to-residue correspondence for two proteins having superposable parts of the backbone conformations.