Re: [gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?
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 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 > Subject: [gmx-users] Domain Motion => How do get the rotational axis >fromeigenvectors ? > To: gmx-users@gromacs.org > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Hi > I want to protein's domain motion. > I use g_covarandg_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 > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110526/9dde6334/attachment-0001.html > > -- > > Message: 2 > Date: Fri, 27 May 2011 05:54:07 +0200 > From: Tsjerk Wassenaar > Subject: Re: [gmx-users] Domain Motion => How do get the rotational >axis from eigenvectors ? > To: Discussion list for GROMACS users > Message-ID: > 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 > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?
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 Subject: [gmx-users] Domain Motion => How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi I want to protein's domain motion. I use g_covarandg_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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110526/9dde6334/attachment-0001.html -- Message: 2 Date: Fri, 27 May 2011 05:54:07 +0200 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ? To: Discussion list for GROMACS users Message-ID: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?
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 On Fri, May 27, 2011 at 4:54 AM, Chih-Ying Lin wrote: > > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?
Hi I want to protein's domain motion. I use g_covarandg_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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
