[gmx-users] Plotting B-factor

[David van der Spoel]

Kukol, Andreas wrote:
> Use the -res option for g_rmsf to calculate the average for each residue. But beware: the experimental B-factor is defined for atoms.
> 
This is true for most cases, but sometimes, in particular for low 
resolution structures when there is not a lot of data, refinement may be 
done with one b-factor for an entire helix. Therefore one should ALWAYS 
read the paper describing the experimental structure.

> Andreas
> 
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] 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.
> 
> Muhammad Alif Mohammad Latif
> Department of Chemistry
> Faculty of Science
> Universiti Putra Malaysia
> 43400 UPM Serdang, Selangor
> MALAYSIA
> 
> 
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-- 
David van der Spoel, Ph.D.
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