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Re: Procedure for approving small dictionary updates
- To: James Hester <jamesrhester@gmail.com>
- Subject: Re: Procedure for approving small dictionary updates
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 19 Aug 2009 20:53:54 -0400 (EDT)
- Cc: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard \(COMCIFS\)" <comcifs@iucr.org>
- In-Reply-To: <279aad2a0908191640jf75e95dy65c573579ac85c01@mail.gmail.com>
- References: <279aad2a0908182348l4c20ba88i8b8b5c39cb3287a@mail.gmail.com><20090819062158.L62421@epsilon.pair.com><279aad2a0908191640jf75e95dy65c573579ac85c01@mail.gmail.com>
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 >> ===================================================== > > > > -- > T +61 (02) 9717 9907 > F +61 (02) 9717 3145 > M +61 (04) 0249 4148 > _______________________________________________ > comcifs mailing list > comcifs@iucr.org > http://scripts.iucr.org/mailman/listinfo/comcifs >
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