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superimposing molecules

Clark P. Wells wellsc at platypus.merit.mich.net
Tue Jun 4 09:07:19 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).

   : Thanks in advance.

   : Greg King : gking at arserrc.gov

To which Andrew C.R. Martin replied


   I'd recommend my ProFit program which you can download via my Web
   page.  It should compile on any Unix box and someone has compiled
   it with gcc under DOS.

   It lets you select residue zones, atom type selections, etc and
   should do pretty much everything you want.

   Best wishes,


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.  Since the matrix involved is 3 by 3, the computation is
easy.  The most expensive part is a matrix multiplication (3 by n
times n by 3, with n the number of atoms).

I will be happy to discuss the method via e-mail -- note my correct
e-mail address below:

wellsc at river.it.gvsu.edu

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