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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 11:07, 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+''