AMBER Archive (2003)

Subject: Re: helix movement

From: Yuguang Mu (ygmu_at_theochem.uni-frankfurt.de)
Date: Wed Jun 11 2003 - 07:47:34 CDT

Dear Bimo,
After PCA, if you can animate the first 2,3 eigenvectors by VMD or
something else, you can roughly have an idea how this global motion works.
Then you can think out a physical quantity to describe it, for example,
if it looks like coming closer or farther tothe core,
then a distance between the center of mass two group, one from helix and
one from core, can be used to quntitize this mode of motion.

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On Tue, 10 Jun 2003, Bimo Ario Tejo wrote:

> 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
> >
> >
> > --
> >
> > )))))
> > (((((
> > ( O O )
> > -------oOOO--(_)--OOOo-----------------------------------------------------
> > o Wolfgang Andreas Svrcek-Seiler
> > o (godzilla)
> > svrci_at_tbi.univie.ac.at
> > .oooO Tel.:01-4277-52733
> > ( ) Oooo.
> > -------\ (----( )--------------------------------------------------------
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> >
> >
>
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