superimposing molecules

Ira Ropson iropson at bcmic.hmc.psu.edu
Sat Dec 7 16:21:41 EST 1996


Hi world,

I would like to superimpose three structures in the same family of
proteins for comparison purposes for a paper I'm writing on the folding
of proteins having considerable sequence heterogeneity but very similar
X-ray structures. The proteins are intestinal fatty acid binding
protein (131 aa), cellular retinol binding protein 2 (133 aa), and
cellular retinoic acid binding protein (136 aa). I can superimpose them
by eye useing Berkeley RASMAC, and they look pretty good, but I would
like to do a better job by mathematically fitting the backbones of
these proteins to each other. I have insightII available to me on an
SGI, but it states that you have to have the same number of atoms to do
the superposition. Does anyone know of an easy way to do this
(preferably without spending any money)? Is there an easy way to do
this in insightII?

Thanks,
Ira Ropson
iropson at bcmic.hmc.psu.edu
If I had time for a fancy Sig file I problably wouldn't have a job.



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