AMBER Archive (2003)

Subject: Re: helix movement

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Tue Jun 10 2003 - 07:07:49 CDT

Hi,
> Does anyone have a tool to calculate the movement of helix and/or domain from Amber trajectory file? Superimposing some snapshots is useful, but it is not a quantitative way to describe such a movement.
>
> Any help is highly appreciated.
...A nice way to *visualize* helix/domain motions in a coarse-grained
sense is principal component
analysis. I believe the "quasih" program could do the job.
If the dominant contribution to overall structural variation
comes from helix and/or domain movement, one would see that
by 'jumps' of the first principal component.
That's rather qualitative, but nice and might serve as a starting point
for more 'in depth' analysis.
good luck
Andreas 

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