[gmx-users] analyzing beta factor

[Martyn Winn]

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 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.
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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.   *
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