AMBER Archive (2003)

Subject: Re: helix movement

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Tue Jun 10 2003 - 07:18:14 CDT

Dear Andreas,

I have done such a 'qualitative' observation using 2drms plot. With and without the particular domain, 2drms plots show different profile. It looks a 'jump' between them. But the problem now: how to quantisize this movement? My aim is to show that the helix/domain (which creates the protein's lid) is closer or farer from protein core.

Thanks and best wishes,
Bimo
ITB - Stuttgart

----- Original Message -----
From: Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
Date: Tue, 10 Jun 2003 14:07:49 +0200 (CEST)
To: Bimo Ario Tejo <bimo7_at_linuxmail.org>
Subject: Re: helix movement

>
> 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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> (((((
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> o Wolfgang Andreas Svrcek-Seiler
> o (godzilla)
> svrci_at_tbi.univie.ac.at
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