[phenixbb] average temperature factor

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Thu Jul 12 09:24:48 PDT 2012

Hi Pavel,

Yes, I see the baverage in the header of the pdb file. But I would like to
get the baverage for the different chains in  the structure. I tried using
"phenix.pdbtools model.pdb model_statistics=true" on separate chains, but I
don't get a value for Baverage from this.


On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Ursula,
>  Is there an easy way to calculate average temperature factors in phenix
>> or another program after ADP + TLS refinement in phenix?
> yes. If you PDB file is after phenix.refine run, then the average ADP is
> reported in PDB file header as well as in refinement log file.
> For a PDB file you can calculate average ADP using this command:
> phenix.pdbtools model.pdb model_statistics=true
> It does not matter where PDB file come from as long as ATOM or/and ANISOU
> records contain the correct ADPs.
> Pavel
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Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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