superimposing molecules

David Jones jones at bsm.bioc.ucl.ac.uk
Wed Jun 5 12:16:10 EST 1996


Andrew Dalke (dalke at ks.uiuc.edu) wrote:

: 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.

Well, it's a commonly used method, granted, but I don't think there is
a "standard" way to superpose two structures. It's not much different
from the variety of methods for curve-fitting, matrix diagonalization, or
just about any numerical computing problem.

I must have seen at least 10 papers (and there must be more) in Acta Cryst
detailing different ways of skinning this particular cat - Andrew McLachlan
has published two alternatives, for example - one based on U matrix
diagonalization (1979) and one based on conjugate gradient minimization
(1982). Just doing a quick scan through the program codes on my
machine here, I can see at least 5 different approaches used by
different authors. I guess some must be quicker than others, some more
stable as the equivalent points approach colinearity, but they all seem
to work OK in the applications concerned.

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