Hey Yuri, What do you mean with mean? Mean without fitting is a single point. Mean only makes sense after aligning. Now there's a nice recursive problem: 1. Calculate mean to get reference 2. Align to reference to calculate mean (http://xkcd.com/754/)
But think about it... aligning to some reference is good enough to fix the mean and the covariance matrix. :) Cheers, Tsjerk On Tue, Aug 16, 2011 at 11:16 AM, Yuri Garmay <yuri.from....@gmail.com> wrote: > I know, but the best reference is "mean". And it is another mean that > calculated after fit at some frame. > > 2011/8/16 Tsjerk Wassenaar <tsje...@gmail.com> >> >> Hi, >> >> > This questuion may be hard. You need rabbi's advice)) >> > But there are some feature of the reference structure that makes it good >> > or >> > bad. It is mean deviation of the atomic coordinates of the fited >> > structures >> > from the reference, the best reference minimizes this measure. For a >> > rigid >> > structure it is acceptable choice to use first or any other frame, but >> > for a >> > flexible it can produce misfit and tangible distortion of the >> > conformations' >> > relations. >> >> The reference is used to align the system, not to calculate the >> deviations, unless explicitly specified to do so, which usually does >> not make sense. I've commented on that on the list on several >> occasions. Taking the first frame, or the last or another is all fine. >> Just as long as the same reference is used for all trajectories that >> are to be compared. >> >> Cheers, >> >> Tsjerk >> >> > >> > Yuri. >> > >> > -- >> > 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 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 > > > -- > 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 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