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super aligns two selections. super is more robust and accurate than align. For syntax, see align.

Algorithm Details

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+''

See Also