Ah yes, of course. I keep forgetting these strange units ;-) m On Wed, 2009-02-04 at 11:16 +0100, David van der Spoel wrote: > Martyn Winn wrote: > > The factor is 8 * pi^2 > > The 100 comes from nm to Angstrom. > > > 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) > Only when writing to a pdb file. > > > > > 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 > >> > > > -- > 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 -- *********************************************************************** * * * 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
