Super

Overview

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

Algorithm Details

super does a BLAST-like BLOSUM62-weighted dynamic programming sequence 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). Next, it does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy.

Caveats

• If super ever tells you no matched atoms, then instead of

super p1, p2

try

super p1 & alt A+'', p2 & alt B+''

See Also

• align
• Cealign