Re: [PyMOL] alignment algorithms

[Jason V. <jas...@sc...>]

> 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) Jas...@sc...
(o) +1 (603) 374-7120