[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

[Chih-Ying Lin]

Hi
I want to get the rotational axis about the protein domain motion.
*From the DynDom website => "DynDom* is a program to determine domains,
hinge axes and hinge bending residues in proteins where two conformations
are available."

Questions:
1. Do the hinge axes represent the rotational axis about the protein domain
motion ?
2. From its User created database, domains and hinge bending residues,
rotation angles and translation are created.
    => The rotation angles must be defined as the angle of rotation between
two domains based on the hinge axes, right ?
    => The vector of the hinge axes is not given by DynDom website, or I did
not find it ???
    => Hinge axes could be obtained from hinge bending axes residues, right
????  If so, How ????
    => How can I get the vector of the hinge axes with the results from
DynDom ???
    => I found some papers drawing the hinge axes, can Gromacs help me find
and draw the hinge axes ????
    => From User created database in the DynDom website, it is showing
"Sequence". What does sequence represent ???
3. Should I install the program of DynDom and then g_dyndom can be
functioned ???
    (we need to install DSSP before using do_dssp)
4. From Gromacs manual => "The purpose of this program (g_dyndom) is to
interpolate and extrapolate the rotation as found by DynDom."
   What does it mean "to interpolate and extrapolate the rotation as found
by DynDom" ?


Thank you
Lin






Message: 1
Date: Thu, 26 May 2011 19:54:29 -0700
From: Chih-Ying Lin <chihying2008 at gmail.com>
Subject: [gmx-users] Domain Motion => How do get the rotational axis
       from    eigenvectors ?
To: gmx-users at gromacs.org
Message-ID: <BANLkTinje0FHG6e1DsO8aJ66_N16XncO+Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi
I want to protein's domain motion.
I use   g_covar    and    g_anaeig  to get the eigenvectors.
How can i get the rotational axis of which protein do its domain motion from
those eigenvectors?

I found the papers and the authors plot its rotational axis of domain
motion.
How did they make it ?


Thank you
Lin
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Message: 2
Date: Fri, 27 May 2011 05:54:07 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Domain Motion => How do get the rotational
       axis from       eigenvectors ?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BANLkTinKF=-c5+M7op80Dy2VaFM=ML4AFg at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Lin,

You don't get such axes directly from covariance analysis. If you want
to know which rotations are associated with a certain eigenvector, you
have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/)
on the extreme projections of your trajectory onto an eigenvector.

Cheers,

Tsjerk
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