[gmx-users] analyzing beta factor

[David van der Spoel]

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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-- 
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