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 SŪ III
>>
>> <div>-------- Original message --------</div><div>From: Chen Zhao <[log in to unmask]> </div><div>Date:10/04/2014 4:03 PM (GMT-05:00) </div><div>To: PHENIX user mailing list <[log in to unmask]> </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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>>
