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Re: Procedure for approving small dictionary updates

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

loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.country
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_publisher
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary 'The structure of 2Zn pig insulin crystals at 1.5 A resolution.'
Philos.Trans.R.Soc.London,Ser.B                          319 369 456 1988 
PTRBAE UK 0080-4622     0441 ?
2905485 ?

_cell.pdbx_unique_axis   ?

_symmetry.pdbx_full_space_group_name_H-M   ?

loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.details
1 polymer     man 'INSULIN (CHAIN A)' 2383.700 2   ?
2 polymer     man 'INSULIN (CHAIN B)' 3403.955 2   ?
3 non-polymer syn 'ZINC ION'          65.380   2   ?
4 water       nat water               18.015   350 ?

loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
1 'polypeptide(L)' no no GIVEQCCTSICSLYQLENYCN 
GIVEQCCTSICSLYQLENYCN          A,C
2 'polypeptide(L)' no no FVNQHLCGSHLVEALYLVCGERGFFYTPKA 
FVNQHLCGSHLVEALYLVCGERGFFYTPKA B,D

....

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
=====================================================

On Thu, 20 Aug 2009, James Hester wrote:

> On Wed, Aug 19, 2009 at 8:31 PM, Herbert J.
> Bernstein<yaya@bernstein-plus-sons.com> wrote:
>> Two problems:
>>
>> This system defaults to approval even if there is no comment; and
>
> Yes, but remember that the relevant DMG will have already discussed
> and approved (explicitly) the proposal; in this case it is reasonable
> to default to approval.
>
>> The time limits are too short for the summer, when people may be away
>> for a full month and need to catch up after that.
>>
>> I would suggest the default change from automatic approval, to "expedited
>> approval" by the COMCIFS chair or designee if no objection is raised to
>> such handling withing 6 weeks of entry on the COMCIFS discussions list.
>
>> This would allow more time for people who are away for full month to ctach
>> up on their email and would ensure that at least one person (the COMCIFS
>> chair or designee) had to actually read and think about and say something
>> about the proposal before it was approved.
>
> I have no objections to these changes.  Note that the COMCIFS chair
> would actually coordinate posting the final proposal from the DMG to
> COMCIFS, so would in any case be aware of the proposal, but your
> suggested change has the advantage of explicitly requiring a formal
> statement from the chair (or designee).
>
> A six-week time limit should apply to the present discussion as well,
> given that we are in the northern summer at the moment.
>
>> I would suggest this proposal be applied to all dictionaries, including
>> mmCIF, imgCIF and pdbx.
>
> 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.
>
> best wishes,
> James.
>
>> 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
>> =====================================================
>
>
>
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