Well, if you simply replace that "beauty" by this one:
grep "^ATOM" filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print s/NR;}'
You will achieve exactly the same result (the b-factors are in the 15th field of the _atom_site section in deposited mmCIF files). I'm not an expert in awk, but I'm sure that can be made even shorter ;)
It is important to keep in mind that mmCIF files are designed to be usable with grep-like tools, so I don't see any problems in moving forward to that format. Whilst I see a lot of problems in staying with the classic PDB format.
Cheers Jose On 05.10.2014 11:18, Tim Gruene wrote:
Hi all, reading this beauty I would like to ask a question to the respective developers: 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? Best, Tim 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.z...@yale.edu> </div><div>Date:10/04/2014 4:03 PM (GMT-05:00) </div><div>To: PHENIX user mailing list <pheni...@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 _______________________________________________ phenixbb mailing list pheni...@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb
