Difference between revisions of "Super"
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=== Algorithm Details === | === 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. | '''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 | ||
| + | <source lang="python"> | ||
| + | super p1, p2 | ||
| + | </source> | ||
| + | try | ||
| + | <source lang="python"> | ||
| + | super p1 & alt A+'', p2 & alt B+'' | ||
| + | </source> | ||
| + | |||
| + | == See Also == | ||
| + | * [[align]] | ||
| + | * [[Cealign]] | ||
| + | |||
| + | |||
| + | [[Category:Commands]] | ||
Revision as of 12:07, 17 July 2009
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+''