[phenixbb] average temperature factor

Christian Roth christian.roth at bbz.uni-leipzig.de
Thu Jul 12 09:31:30 PDT 2012


Hi Ursula,

probably there exist also a trick in phenix, but another option would be 
moleman from Uppsala. It prints B values for chains or for the type of 
atom/residue.

Christian
Am Donnerstag 12 Juli 2012 18:24:48 schrieb Ursula Schulze-Gahmen:
> 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> 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
> > http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online
> >.org/mailman/listinfo/phenixbb>
> 


-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
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04103 Leipzig
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