> Dear Jason, > > ""super" does pairwise residue alignments followed by a superposition. > It also does refinements to improve the overall quality." > > Could you elaborate a little more on this? Do you mean that it > calculates all pairwise distances and does a least squares fit with > refinement steps that toss out any atoms that are more than 2 standard > deviations from the mean residue-residue rmsd, or something more > complex? > > Thank you,
Michael, "Super" does pairwise residue comparisons using a difference of distance matrices (as is common in other methods). It then builds the highest scoring alignment by taking the best scoring match, with or without gaps, and window averaging, using a dynamic programming style search for all possible pairs. Think of doing a Needleman-Wunsch, but on structural scores instead of a sequence scoring matrix (BLOSUM62). FYI, there is an infrequently discussed "window" parameter which will consider not just diff(atomA, atomB) but considers local substructure as large as the window you provide: fetch 1rlw 1rsy, async=0 super 1rlw, 1rsy, window=0 # now compare to super 1rlw, 1rsy, window=8 This window feature is used in other algorithms for considering average substructure, not just pairwise scores. Try "help super" for more information on the parameters. Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
