[phenixbb] Calculate average B-factor?

Tim Gruene tg at shelx.uni-ac.gwdg.de
Sun Oct 5 02:18:20 PDT 2014

Hi all,

reading this beauty I would like to ask a question to the respective
Will the PDB format remain the working format for the users and only
upon deposition will it be converted to PDBml for archiving purposes, or
are the refinement programs (et al.) going to abandon PDB, too?


On 10/04/2014 10:32 PM, Ed Pozharski wrote:
> grep "^ATOM  " filename.pdb | cut -c 61-66 | awk '{s+=$1;} END {print s/NR;}'
> "Nobody likes a show off, Private"
>                                            Skipper
> Cheers
> Sent on a Sprint Samsung Galaxy S® III
> <div>-------- Original message --------</div><div>From: Chen Zhao <c.zhao at yale.edu> </div><div>Date:10/04/2014  4:03 PM  (GMT-05:00) </div><div>To: PHENIX user mailing list <phenixbb at phenix-online.org> </div><div>Subject: [phenixbb] Calculate average B-factor? </div><div>
> </div>Dear all,
> I am just wondering whether there is a command line tool in phenix that calculates the average B-factor of a PDB file? Can it deal with the ANISOU records (from TLS refinement or not) properly? I looked into previous posts but the  --show-adp-statistics option in phenix.pdbtools seems to be no longer available in the version (1.9-1678) I installed.
> Thank you so much,
> Chen
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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