Re: [PyMOL] Algorithm for pyMOL's fit and rmsd algorithms

[Warren D. <wa...@de...>]

Vince,

I apologize, but I do not know its ultimate source -- that minimal RMSD
fitting code has been floating around my toolkit for years.  My personal
belief is that the approach is equivalent to Kabsch yet stable with
respect to degenerate cases (e.g. all points in a plane).  However, I
have neither the linear algebra chops nor the time to prove it.

The reference for Kabsch is here:

Kabsch, Wolfgang, (1976) "A solution of the best rotation to relate two
sets of vectors", Acta Crystallographica 32:922.

Of course, if anyone ever comes across a case where PyMOL performs
noticably worse than Kabsch, we would certainly like to know about it!  

Cheers,
Warren

> -----Original Message-----
> From: Vincent Chu [mailto:vin...@st...]
> Sent: Tuesday, January 20, 2009 1:14 PM
> To: pym...@li...
> Subject: [PyMOL] Algorithm for pyMOL's fit and rmsd algorithms
> 
> Hi all --
> 
> I've been using pyMOL's fit and rmsd commands on small numbers of
> structures but now I'd like to use these functions on large numbers of
> molecules.
> 
> Does anybody know what algorithm is used in pyMOL to superimpose
> molecular structures on top of other ones (i.e., pymol's fit
> function). Better yet would be a reference.
> 
> Thanks!
> 
> Vince
> 
> --
> ------------------------
> Vincent Chu
> Department of Applied Physics
> Geballe Laboratory of Advanced Materials
> McCullough Bldg. 318
> 476 Lomita Mall
> Stanford, CA, 94305-4045
> 
> vincentc [at] stanford.edu
> http://www.stanford.edu/~vincentc/
> 415.279.7733
> 
> "Join a group. Get an identity."
> 
>
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