[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.
Pavel
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
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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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