Linda, It is not a published algorithm except in the sense that the implementation is open-source. In a nutsheel:
"align" 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). "super" does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected] > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Lu Lin > Sent: Friday, January 25, 2008 4:29 AM > To: [email protected] > Subject: [PyMOL] algorithm for alignment > > Hi all, > > Anyone know which algorithm PyMOL uses to align or super of > two structures? > > Thanks a lot! > > Best, > Linda > > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users
