Software for superposition of similar molecules/domains

Kay Diederichs dikay at
Fri Jan 13 05:40:31 EST 1995

Rick Faber (R.Faber at wrote:
: Anyone know of a 'automated' way of doing superpositions of different 
: molecules other than using O?  I'd just like to save a little of the
: drugery of figuring which C-alphas should correspond to which in 
: several different domains/molecules.  Someone must have written code to 
: do this somewhere.....  Any hints would be appreciated.

: cheers,
: Rick

: R.Faber at


if you need a program that figures out for you which Calpha in one molecule
corresponds to which Calpha in the other molecule, and superimposes the
two molecules based on the equivalent residues it found, I'll be happy to send
my program 'superimpose' to you. It's about 600 lines of standard Fortran
code and takes a few minutes of CPU time on a fast workstation for two 
proteins of medium size. 

My program doesn't do least-squares superposition, but you can do that easily 
in 'O',after defining a suitable unity matrix to start with by:
db_create .lsq_rt_unity 12 R db_set_data .lsq_rt_unity 9 9 1.
db_set_data .lsq_rt_unity 5 5 1.  db_set_data .lsq_rt_unity 1 1 1.
lsq_improve unity mola ; molb ;; molb2mola
assuming mola and molb are the names of your molecules. 

Kay Diederichs                      email: dikay at 
Universitaet Freiburg, Institut fuer Biophysik, Albertstr. 23 
D-79104 Freiburg, Germany   Tel. +49/(0)761/2035391 FAX +49/(0)761/2035016

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