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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Alif M Latif
Sent: 02 May 2008 09:42
To: [email protected]
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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