On Sun, 5 Oct 2014 13:13:14 +0200, Jose Manuel Duarte <[email protected]>
wrote:
>Well, if you simply replace that "beauty" by this one:
>
>grep "^ATOM" filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
>s/NR;}'
>
the problem with this is that it will break if there is any B-factor of 100 or
higher, because then the blank will be missing ...
Kay
>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
>>> <[email protected]> </div><div>Date:10/04/2014 4:03 PM (GMT-05:00)
>>> </div><div>To: PHENIX user mailing list <[email protected]>
>>> </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
>>> [email protected]
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
