superimposing molecules

Christoph Steinbeck stein at
Sun Dec 8 14:21:04 EST 1996

Andrew Dalke wrote:
> > 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
> >    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  :)
> ( 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.

I found VMD to be a incredibly useful and versatile tool for
visualisation and analysis of molecular structures - all I'm missing is
exactly this one feature of superimposing a set of structures (let's say
ten, not only two).
So, Andrew, did I get you right, that this is possible? 
And if so, how can I do it? The manual states, one can do it with two
What do you mean by: "...any set of your choice"?

Regards, Chris

Dr. Christoph Steinbeck - PGP available on my homepage
mailto:stein at  -
Dep. of Chemistry, Tufts Univ., 62 Talbot Ave., Medford, MA 02155, USA
Phone: int + (617) 627-3881      FAX: int + (617) 627-3443

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