[gmx-users] analyzing beta factor

[David van der Spoel]

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