Yes, that's what I'd like. great, thanks for the suggestion, Arneh
> If you want a structure representative for your trajectory, rather > than the average, I suggest using g_cluster to cluster your frames > and take the cluster center from the largest cluster. > > /Erik > > 20 sep 2007 kl. 17.18 skrev Arneh Babakhani: > >> Great, got it, thanks for the suggestion, appreciate the input, >> >> Arneh >> >>> Arneh Babakhani wrote: >>>> Hi, >>>> >>>> When outputting the average structure from g_rmsf using the -ox >>>> option, >>>> some of my residues in that average structure pdb have awkward >>>> coordinates >>>> (when you visualize it in VMD, it looks very strange). Sometimes >>>> atoms >>>> are placed very close to each other, with really bad bond angles. I >>>> suppose this is a facet of the averaging scheme in g_rmsf. >>> >>> Yes. If you ask for an not-necessarily-physical result, you >>> usually get >>> one... see http://wiki.gromacs.org/index.php/Average_Structure >>> >>>> Is there a way to correct for this, and to obtain an >>>> averagestructure.pdb >>>> that looks more reasonable coordinates and bond angles? (I ask b/ >>>> c I'd >>>> like to use this averagestructure.pdb in further studies, such as >>>> docking.) >>> >>> "Correcting for" is not quite the right phrasing here... :-) It's >>> already correct according to the algorithm you used... it's not the >>> algorithm's fault you actually wanted a physical structure. One >>> approach >>> you can use is to select the structure with the smallest RMSD from >>> the >>> average, kind of like selecting the median as the central measure >>> rather >>> than the mean of a numerical data set. Or you can take the >>> nonphysical >>> structure and do EM on it... One needs to apply brain, of course! >>> >>> Mark >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
