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 chihying2...@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 chihying2...@gmail.com Subject: [gmx-users] Domain Motion = How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: banlktinje0fhg6e1dso8aj66_n16xnc...@mail.gmail.com 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 tsje...@gmail.com Subject: Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTinKF=-c5+M7op80Dy2VaFM=ml4...@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 -- 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 chihying2...@gmail.com Subject: [gmx-users] Domain Motion = How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: banlktinje0fhg6e1dso8aj66_n16xnc...@mail.gmail.com 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 tsje...@gmail.com Subject: Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTinKF=-c5+M7op80Dy2VaFM=ml4...@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 -- 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
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 chihying2...@gmail.com 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
