super aligns two selections. super is more robust and accurate than align. For syntax, see align.
super does a sequence-independent structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance).
- If super ever tells you no matched atoms, then instead of
super p1, p2
super p1 & alt A+'', p2 & alt B+''