<html><body bgcolor="#FFFFFF"><div><br></div><div>You should a have good read at the original papers. They are mentioned on the web site. They will answer all your questions. <br><br>On May 28, 2011, at 6:03, Chih-Ying Lin <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div><br>Hi<br>I want to get the rotational axis about the protein domain motion. <br><b>From the DynDom website => "DynDom</b> is a program to determine domains, hinge axes and hinge
bending residues in proteins where two conformations are available."<br><br>Questions: <br>1. Do the hinge axes represent the rotational axis about the protein domain motion ? <br>2. From its User created database, domains and hinge bending residues, rotation angles and translation are created. <br>
=> The rotation angles must be defined as the angle of rotation between two domains based on the hinge axes, right ?<br> => The vector of the hinge axes is not given by DynDom website, or I did not find it ???<br>
=> Hinge axes could be obtained from hinge bending axes residues, right ???? If so, How ????<br> => How can I get the vector of the hinge axes with the results from DynDom ???<br> => I found some papers drawing the hinge axes, can Gromacs help me find and draw the hinge axes ????<br>
=> From User created database in the DynDom website, it is showing "Sequence". What does sequence represent ???<br>3. Should I install the program of DynDom and then g_dyndom can be functioned ??? <br> (we need to install DSSP before using do_dssp) <br>
4. From Gromacs manual => "The purpose of this program (g_dyndom) is to interpolate and extrapolate the
rotation as found by DynDom." <br> What does it mean "to interpolate and extrapolate the rotation as found by DynDom" ?<br><br><br>Thank you<br>Lin<br><br><br><br><br><br><br>Message: 1<br>
Date: Thu, 26 May 2011 19:54:29 -0700<br>
From: Chih-Ying Lin <<a href="mailto:chihying2008@gmail.com"><a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a></a>><br>
Subject: [gmx-users] Domain Motion => How do get the rotational axis<br>
from eigenvectors ?<br>
To: <a href="mailto:gmx-users@gromacs.org"><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></a><br>
Message-ID: <<a href="mailto:BANLkTinje0FHG6e1DsO8aJ66_N16XncO%2BQ@mail.gmail.com"><a href="mailto:BANLkTinje0FHG6e1DsO8aJ66_N16XncO+Q@mail.gmail.com">BANLkTinje0FHG6e1DsO8aJ66_N16XncO+Q@mail.gmail.com</a></a>><br>
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<br>
Hi<br>
I want to protein's domain motion.<br>
I use g_covar and g_anaeig to get the eigenvectors.<br>
How can i get the rotational axis of which protein do its domain motion from<br>
those eigenvectors?<br>
<br>
I found the papers and the authors plot its rotational axis of domain<br>
motion.<br>
How did they make it ?<br>
<br>
<br>
Thank you<br>
Lin<br>
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Message: 2<br>
Date: Fri, 27 May 2011 05:54:07 +0200<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com"><a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a></a>><br>
Subject: Re: [gmx-users] Domain Motion => How do get the rotational<br>
axis from eigenvectors ?<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org"><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></a>><br>
Message-ID: <BANLkTinKF=-c5+M7op80Dy2VaFM=<a href="mailto:ML4AFg@mail.gmail.com"><a href="mailto:ML4AFg@mail.gmail.com">ML4AFg@mail.gmail.com</a></a>><br>
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<br>
Hi Lin,<br>
<br>
You don't get such axes directly from covariance analysis. If you want<br>
to know which rotations are associated with a certain eigenvector, you<br>
have to run a routine like dyndom (<a href="http://fizz.cmp.uea.ac.uk/dyndom/" target="_blank"><a href="http://fizz.cmp.uea.ac.uk/dyndom/">http://fizz.cmp.uea.ac.uk/dyndom/</a></a>)<br>
on the extreme projections of your trajectory onto an eigenvector.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
</div></blockquote><blockquote type="cite"><div><span>-- </span><br><span>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></a></span><br><span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br><span>Please don't post (un)subscribe requests to the list. Use the </span><br><span>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.</span><br><span>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"><a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></a></span></div></blockquote></body></html>