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 <[email protected]>
Subject: [gmx-users] Domain Motion => How do get the rotational axis
from eigenvectors ?
To: [email protected]
Message-ID: <[email protected]>
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 <[email protected]>
Subject: Re: [gmx-users] Domain Motion => How do get the rotational
axis from eigenvectors ?
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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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