The factor is 8 * pi^2 The factor 1/3 arises when you take the trace of an anisotropic displacement parameter. But I believe g_rmsf will do this conversion anyway with options -oq or -ox (I've not tested this, just read the documentation)
Cheers Martyn On Wed, 2009-02-04 at 09:05 +0100, David van der Spoel wrote: > özge kül wrote: > > From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Alif M Latif > > Sent: 02 May 2008 09:42 > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Plotting B-factor > > > > Dear GROMACS users and developers, > > > > I want to plot B-factor of a protein structure against residue. How can I > > do > > that?. Using option -oq in g_rmsf only produce bfac.pdb which is in .pdb > > file > > and assigned at each atom. Is there another way I can get the plot B-factor > > vs > > residue?. Any link to example or tutorial will be very helpful. > > Comments and Suggestions are greatly appreciated. Thank you. > Take the g_rmsf -res output, square it and multiply it by (IIRC) 800 > pi^2/3 (you can do all this in xmgrace). Check the factor. > > > > Muhammad Alif Mohammad Latif > > Department of Chemistry > > Faculty of Science > > Universiti Putra Malaysia > > 43400 UPM Serdang, Selangor > > MALAYSIA > > > > > > > > --- On *Wed, 2/4/09, David van der Spoel /<sp...@xray.bmc.uu.se>/* wrote: > > > > From: David van der Spoel <sp...@xray.bmc.uu.se> > > Subject: Re: [gmx-users] analyzing beta factor > > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > > Date: Wednesday, February 4, 2009, 2:16 AM > > > > özge kül wrote: > > > Hi users, > > > > > > I want to plot beta factor versus residue number plot at the analyzing > > part.I read manual and search in the web but I could not find a > > reasonable > > result for this plot.I wonder if anybody know about it. > > > > > What is the beta factor? > > > > > > > Thank you, > > > Özge > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > 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 gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- David van der Spoel, Ph.D., Professor of Biology > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *********************************************************************** _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
