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

[XAvier Periole]

You should a have good read at the original papers. They are mentioned on the web site. They will answer all your questions. 

On May 28, 2011, at 6:03, Chih-Ying Lin <chihying2008 at gmail.com> wrote:

> 
> 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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