superimposing molecules

Paul Sanschagrin sanschag at
Sun Dec 8 13:19:04 EST 1996

Ira Ropson wrote:
> 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
> If I had time for a fancy Sig file I problably wouldn't have a job.

What you could do is to superimpose the overlapping residues in both.
If you've done it by eye, you probably have a good estimate as where
the starting and ending points of comparison should be. InsightII will
allow you to superimpose only portions of the sequence by including
them as molcule_name:start end (e.g. POR:35-126). If you choose to
do backbone atoms only (or alpha carbons) and include the same number
of residues in both, this should work fine. Let me know if I can
be of more help.

				Paul Sanschagrin
				sanschag at
Those people who tell you not to take chances
They are all missing on what life is about
You only live once so take hold of the chance
Don't end up like the others, the same song and dance
			 from "Motorbreath", _Kill 'Em All_

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