[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?
x.periole at rug.nl
Sat May 28 11:10:06 CEST 2011
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:
> 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."
> 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
> 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"
> 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
> How did they make it ?
> Thank you
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> 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>
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> 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.
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