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superimposing molecules

Andrew Dalke dalke at ks.uiuc.edu
Tue Jun 4 09:59:33 EST 1996

>Gregory King (GKING at ARSERRC.GOV) wrote: : Greetings,
>   I'm looking for software (or an explanation of an efficient
>   algorithm) that will superimpose molecule A onto molecule B with
>   a combination of translations and rotations, and using a minimal
>   rms deviation as the convergence criterion.  There is a known
>   one-to-one correspondence between the relevant atoms in both
>   molecules (I'll be comparing peptides, and using the backbone atoms
>   as the relevant ones).

To which wellsc at river.it.gvsu.edu responded:
> I would point out that an iterative method is not necessary, and in
> fact is wasteful of computing time.  A method which has been known in
> robotics for at least ten years uses the singular value decomposition
> of a 3 by 3 matrix to yield a closed form (rather than iterative)
> procedure.

I thought the standard way to do rmsd best-fit alignment of two structures
with 1-1 assignment, as in Kabsch, Acta Cryst. (1978) A34, 827-828,
and that's what I used in our visualization program, VMD.  It isn't
iterative and works fine as far as I can see.

						dalke at ks.uiuc.edu

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