superimposing molecules

Paul Sanschagrin sanschag at sol.bch.msu.edu
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 bcmic.hmc.psu.edu
> 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 sol.bch.msu.edu
				http://www.msu.edu/user/sanschag/
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