AMBER Archive (2004)

Subject: AMBER: Plot B-factor extracted from PDB file

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Wed Oct 13 2004 - 09:41:29 CDT

Drs Cheatham, Ross,
Thanks for the instrcutions about the MD sampling and benchmarking! It is
very helpful.

The question is kind of trivial........I want to plot the experimental
B-factor in order to compare with that calculated from MD (by residues). How
can I easily extract the B-factors from PDB x-ray strucutre (comparable with
the mass-weighted Bfactor form MD)?

Thank you for help.

Xin

>
> The program ptraj can calculate atomic positional fluctuations or
> B-factors. To do this, you need to RMS fit the trajectory to a common
> reference frame and use the atomicfluct command.
>
> trajin mdcrd.1
> trajin mdcrd.2
> rms first mass out backbone_rms.dat @C,CA,N
> atomicfluct out bfactor_byres.dat :1-200 byres bfactor
>
> The above assumes the protein is residues 1-200.
>
>
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