Thanks Frances for the explanation. Indeed mmCIF format is a lot more
complicated and grep can be a dangerous tool to use with them. But for
most cases it can do the job and thus it maintains some sort of
backwards compatibility. I can't agree more that using specialised tools
(for either PDB files or mmCIF files) that deal with the formats
properly is the best solution (see for instance
http://mmcif.wwpdb.org/docs/software-resources.html for some of the
mmCIF readers).
In any case I find it most surprising that this topic came yet again to
this BB, when it was thoroughly discussed last year in this thread:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=ccp4bb&D=0&P=26939
I'm not sure why this kind of urban legends on the evilness of the mmCIF
format keep coming back to the list...
As explained there and elsewhere endless times, the PDB format is
inadequate to represent the complexity of macromolecules and has been
needing a replacement for a long time. The decision to move on to mmCIF
has been made and in my opinion the sooner we move forward the better.
Cheers
Jose
On 05.10.2014 15:52, Frances C. Bernstein wrote:
mmCIF is a very general format with tag-value pairs, and loops
so that tags do not need to be repeated endlessly. It was
designed so that there is the flexibility of defining new terms
easily and presenting the data in any order and with any kind
of spacing.
I understand that there are 100000+ files in cyberspace prepared
by the PDB and that they all have the 'same' format.
It is tempting to write software that treats these files as fixed
format and hope that all software packages that generate coordinate
files will use the same fixed format. But that loses the generality
and flexibility of mmCIF, and software written that way will fail
when some field requires more characters or a new field is added.
There are software tools to allow one to read and extract data from
any mmCIF file; using these is more complicated than using grep but
using these assures that one's software will not fail when it encounters
a date file that is not exactly what the PDB is currently producing.
Note that mmCIf was defined when the limitations of the fixed-format
PDB format became apparent with large structures. Let's not repeat
the mistakes of the past.
Frances
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On Sun, 5 Oct 2014, Tim Gruene wrote:
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 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
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