superimposing molecules

[Andrew Dalke]

> Does anyone know of an easy way to do [superposition of molecules]
> (preferably without spending any money)?

There's a couple.  The best is probably ProFit
http://www.biochem.ucl.ac.uk/~martin/text/ProFit.readme

>    ProFit (pronounced Pro-Fit, not profit!) is designed to be the 
> ultimate least squares fitting program and is written to be as easily 
> portable between systems as possible. It performs the basic function 
> of fitting one protein structure to another, but allows as much 
> flexibility as possible in this procedure. Thus one can specify 
> subsets of atoms to be considered, specify zones to be fitted by 
> number, sequence, or by sequence alignment.

And of course I have to plug our visualization program, VMD  :)
(http://www.ks.uiuc.edu/Research/vmd/) which can graphically
align based on all atoms, heavy atoms, or just backbone atoms.
Or, with about 8 lines of scripting language, align based on
any set of your choice.

						Andrew
						dalke at ks.uiuc.edu