[phenixbb] average temperature factor
mbfrolow at post.tau.ac.il
Sat Jul 14 23:09:39 PDT 2012
I get it! in my case it is a right click!!! :-)
On Jul 13, 2012, at 22:10 , Nathaniel Echols wrote:
> 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
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