Re: helix movement

From: Andreas Svrcek-Seiler <>
Date: Tue, 10 Jun 2003 14:07:49 +0200 (CEST)

> 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

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Tue Jun 10 2003 - 13:53:01 PDT
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