[phenixbb] average temperature factor

Pavel Afonine pafonine at lbl.gov
Thu Jul 12 09:49:41 PDT 2012

Hi Ursula,

here is a solution, not nice though:

step 1: get a pdb file with chain in question:

phenix.pdbtools model.pdb keep="chain A" output.file_name="chain_A.pdb"

step 2: then this will give you average B

phenix.pdbtools chain_A.pdb model_statistics=true

Other suggestions (by David & Christian) might work too, but I have no 
idea how these programs handle TLS contribution to ADP and ANISOU 
records. Though since phenix.refine outputs total ADPs I guess this 
should be just fine.


On 7/12/12 9:24 AM, Ursula Schulze-Gahmen wrote:
> 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.
> Ursula
> On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto: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
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
> _______________________________________________
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