[phenixbb] average temperature factor

[Nathaniel Echols]

On Thu, Jul 12, 2012 at 9:49 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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.
>

Since this question has come up before, I've added a window for displaying
this in the GUI.  Clicking the magnifying glass icon next to any PDB file
will already open a panel showing an overview of the model contents, and
now there will also be a button labeled "B-factors by chain" for any file
with multiple chains.  Clicking this button will display the isotropic
B-factors statistics by chain.  Under the circumstances, I'm assuming the
B-factor field in the PDB file is already the total B-factor.

This will be available in the next nightly build.

-Nat
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