Re: [phenixbb] average temperature factor

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 mailto:[email protected]> 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.

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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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