Dear Muhammad, You can plot the rmsf per residue, and calculate the beta factor yourself B = 8*PI^2*RMSF^2/3. Remember to convert from nm to A if you want the same values as in the PDB.
Ran. Alif M Latif wrote: > 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. > > Muhammad Alif Mohammad Latif > > Department of Chemistry > Faculty of Science > Universiti Putra Malaysia > 43400 UPM Serdang, Selangor > MALAYSIA > > > ------------------------------------------------------------------------ > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try > it now. > <http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ%20> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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