Hi Jose,
I see. In the example on page
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/atom_site.html,
it is in field 12, though, and I would have thought that mmCIF allows
line breaks.
But as long as all developers writing PDBx/mmCIF with their programs
follow the PDB constraints (``styling plans'' in their FAQ), everything
is fine.
Cheers,
Tim
On 10/05/2014 01:13 PM, Jose Manuel Duarte 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;}'
>
> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> [log in to unmask]
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
