[gmx-users] analyzing beta factor

[Martyn Winn]

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 at 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 /<spoel at xray.bmc.uu.se>/* wrote:
> > 
> >     From: David van der Spoel <spoel at xray.bmc.uu.se>
> >     Subject: Re: [gmx-users] analyzing beta factor
> >     To: "Discussion list for GROMACS users" <gmx-users at 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
> >     > 
> >     > 
> >     > 
> >     > ------------------------------------------------------------------------
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> > 
> >     -- 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.
> >     spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
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*                                                                     *
*               Dr. Martyn Winn                                       *
*                                                                     *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455    E-mail: martyn.winn at stfc.ac.uk            *
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*             URL: http://www.ccp4.ac.uk/martyn/                      *
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