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Re: Reactivating mmCIF DMG (was discussion of dictionary update procedure)

James and Herbert,

There is an unfortunate confusion in that mmCIF names both a dictionary
and a syntax.  And it is unavoidable that people may identify  the
wwPDB PDBx files as mmCIF files.  However, the wwPDB has long refered
to its data files as compliant with the PDB Exchange Dictionary (PDBx).
The PDB Exchange Dictionary described in the International Tables Volume
G is a recognized extension dictionary which is a superset of mmCIF content
and uses mmCIF syntax.  This dictionary has been developed in conjunction
with the mmCIF dictionary, respecting the mmCIF dictionary organization,
and following the COMCIFs practice of using using a local like pdbx_
to identify extension definitions.   The content of the PDB exchange
dictionary necessarily describes experimental techniques other than
crystallography such as  NMR, EM(3dem_), ..., and  hybrids).  This
dictionary must also provide mappings to the legacy of nomenclature
and conventions in published structures.  Describing this broader
content in a manner that maintains the organization and terminology
in the mmCIF dictionary presents a range of challenges; however,
extensions have been introduced in a manner which as much as possible
preserves the mmCIF schema.

It is important to emphasize that the majority of extension content
in the PDB Exchange dictionary has been added through grass roots
community efforts like COMCIFs and through coordination with other
resources like BMRB and EMDB.  PDB has hosted and resourced the
the mmCIF DMG for many years.  There has admittedly been little
input to this group for a number of years; however, the same can
be said for the other dmg's.   We would certainly welcome and
support new content contributed to the mmCIF dictionary through
this mechanism.

The wwPDB continues to work to provide an archive of data files
with a unified representation of macromolecular structure and
experiment. We would certainly appreciate COMCIFs support in this



On 8/19/09 11:26 PM, James Hester wrote:
> Hi Herbert: I do not dispute that there are also many pdbx tags,
> additional to those for internal use, that have significance for the
> macromolecular community, thus my agreement that we should reactivate
> the mmCIF DMG and look at how to include these.
> James.
> On Thu, Aug 20, 2009 at 12:30 PM, Herbert J.
> Bernstein<yaya@bernstein-plus-sons.com>  wrote:
>> Dear James,
>>   The statement that "the PDB additionally include many 'pdbx' items which
>> have no meaning outside the PDB, but which enable them to freely convert
>> between the database and a CIF file" is incorrect. There certainly are tags
>> in pdbx which are only needed for internal purposes of the PDB, but the
>> issue at hand is not the set of tags for internal use by the pdb, but the
>> very large number of tags from the pdbx dictionary that are essential to the
>> crystallographic description of the molecule.
>>   Consider for example, the secondary structure tags.  The pdbx secondary
>> structure tags are not just some augmentation for database management, they
>> are a major recasting of the approach to secondary structure from the rather
>> elegant approach adopted as part of mmCIF to a compromise between the old
>> PDB secondary structure description and the new mmCIF description.
>>   Consider also, _atom_site.pdbx_PDB_model_num, which is essential to the
>> understanding of multiple model entries, especially because the PDB repeats
>> atom serial numbers between models.  This is not a database management tag.
>>   There are many more such tags.  If they were purely for internal database
>> management, they would not have to be part of every so-called mmCIF entry
>> released by the PDB.  These are, quite literally, de facto standards for
>> crystallographic macromolecular data, and should be carefully considered by
>> the crystallographic community in that context.
>>   I urge everyone to read
>> http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
>>   Regards,
>>     Herbert
>> =====================================================
>>   Herbert J. Bernstein, Professor of Computer Science
>>    Dowling College, Kramer Science Center, KSC 121
>>         Idle Hour Blvd, Oakdale, NY, 11769
>>                  +1-631-244-3035
>>                  yaya@dowling.edu
>> =====================================================
>> On Thu, 20 Aug 2009, James Hester wrote:
>>> To first address Herbert's comments below:  A PDB mmCIF file does
>>> contain a lot of mmCIF data items, so I would argue that calling it an
>>> 'mmCIF' file is reasonable. The PDB additionally include many 'pdbx'
>>> items which have no meaning outside the PDB, but which enable them to
>>> freely convert between the database and a CIF file.  I might add in
>>> passing that this relational database<->  CIF interconvertibility is a
>>> rather remarkable attribute of the CIF standard, and we should
>>> recognise the PDB for the work that they have put into realising this.
>>> It is not correct to state that the 'pdbx' tags are being proposed as
>>> de-facto standards.  If I include 'anbf' tags in powder diffraction
>>> CIF file and call the result a 'pdCIF' file, am I proposing these as
>>> defacto pdCIF standards?  I think not.  I am simply stating that
>>> software that works with pdCIF (eg CMPR) will be able to process this
>>> file.
>>> On the other hand, it is clear that there are plenty of pdbx dataitems
>>> of relevance to the macromolecular community, and work on bringing
>>> these into the mmCIF dictionary would be welcome.  I would certainly
>>> support reactivation of the mmCIF DMG and tasking it with updating
>>> mmCIF.  What do other members think?
>>> Best wishes,
>>> James.
>>> On Thu, Aug 20, 2009 at 10:53 AM, Herbert J.
>>> Bernstein<yaya@bernstein-plus-sons.com>  wrote:
>>>> Dear Colleagues,
>>>> James has written:
>>>>> My understanding is that imgCIF and mmCIF are within the purvey of
>>>>> COMCIFS, but we have no responsibility for pdbx and so this procedure
>>>>> would not apply to it.
>>>>   I am unable to see any justification for exclusion of pdbx, when that,
>>>> rather than mmCIF, is what the PDB uses for its crystallographic
>>>> macromolecular file releases, and even calls those pdbx files mmCIF
>>>> files.
>>>>   For example, when I display the "mmCIF" file for 4ins, I get a file
>>>> that contains the following pdbx items:
>>>> _audit_conform.dict_name       mmcif_pdbx.dic
>>>> _audit_conform.dict_version    1.0670
>>>> _audit_conform.dict_location
>>>> http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
>>>> #
>>>> _pdbx_database_PDB_obs_spr.id               SPRSDE
>>>> _pdbx_database_PDB_obs_spr.date             1990-04-15
>>>> _pdbx_database_PDB_obs_spr.pdb_id           4INS
>>>> _pdbx_database_PDB_obs_spr.replace_pdb_id   1INS
>>>> #
>>>> _pdbx_database_status.status_code    REL
>>>> _pdbx_database_status.entry_id       4INS
>>>> _pdbx_database_status.deposit_site   ?
>>>> _pdbx_database_status.process_site   ?
>>>> _pdbx_database_status.SG_entry       .
>>>> #
>>>> loop_
>>>> _audit_author.name
>>>> _audit_author.pdbx_ordinal
>>>> 'Dodson, G.G.'  1
>>>> 'Dodson, E.J.'  2
>>>> 'Hodgkin, D.C.' 3
>>>> 'Isaacs, N.W.'  4
>>>> 'Vijayan, M.'   5
>>>> ....
>>>> and many, many more
>>>> It is a serious abdication of COMCIFS responsibility to the
>>>> crystallographic
>>>> community for COMCIFS to fail to consider each of the pdbx tags that are
>>>> implicitly being proposed as de facto revisions to the crystallographic
>>>> mmCIF dictionary.
>>>> I propose that a DMG be reactivated for mmCIF and that it be asked by
>>>> COMCIFS to make a proposal to COMCIFs on updating the mmCIF dictionary so
>>>> that it can actually be used for crystallographic macromolecular
>>>> structures.
>>>> Regards,
>>>>   Herbert
>>>> P.S.  An alternative would simply be to discard the mmCIF dictionary,
>>>> inasmuch as it is not being used.
>>>> =====================================================
>>>>   Herbert J. Bernstein, Professor of Computer Science
>>>>    Dowling College, Kramer Science Center, KSC 121
>>>>         Idle Hour Blvd, Oakdale, NY, 11769
>>>>                  +1-631-244-3035
>>>>                  yaya@dowling.edu
>>>> =====================================================
>>> --
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148

   John Westbrook, Ph.D.
   Rutgers, The State University of New Jersey
   Department of Chemistry and Chemical Biology
   610 Taylor Road
   Piscataway, NJ 08854-8087
   e-mail: jwest@rcsb.rutgers.edu
   Ph:  (732) 445-4290  Fax: (732) 445-4320
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