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Re: magCIF - policy advice requested

Hi James,
My issues is only with getting the dictionary definitions into a single DDL.  We routinely use extension dictionarieswhich share a common data model.
Regards,
John

On 5/30/14, 3:53 AM, James Hester wrote:> Hi John W,>> I agree that all the new definitions should be collected together in a single file with a single dictionary dialect.  I do not see> that repeating definitions from core CIF/ms_CIF/symCIF is necessary, given that we do not do that for other extensions to core CIF.> Our point of contention then becomes whether or not, if the dictionary dialect chosen is DDL2, we have to include periods in the> datanames. I say it is not necessary.  If you think that it would be necessary, can you give me some idea of why?  Note that I am> not at all against a particular dictionary (e.g. mmCIF, pdbx) adopting 'dot' notation as a rigorous convention.>> thanks,> James.>> On Wed, May 28, 2014 at 9:25 PM, John Westbrook <jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>> wrote:>>     Hi James,>>     I completely agree with Herbert in this case.  Having all of the data names in a single dictionary with a common>     dialect makes the content much more accessible for users as well as existing software tools.   mmCIF incorporated the core>     definitions with DDL2 naming conventions and aliases.   The core naming conventions were preserved to the extent possible.>     Splitting the definitions across DDL dialects is going to be a significant obstacle to many users at this time.>>     Regards,>>     John>>>>     On 5/28/14, 2:29 AM, James Hester wrote:>>         Hi Herbert,>>         I believe you are advocating duplicating part or all of the modulated structures dictionary (~100 datanames) within the magnetic>         structures dictionary, with aliases as necessary.  As far as I can see, this buys us no more than 'a loop /can/ be written>         so that>>         all datanames have dots in them'.  I do not even say 'must be written', because the aliases mean that you could continue to>         use the>         old-style datanames.>>         Regarding confusion, and the lack of it in the case of mmCIF/core CIF: the presence of two datanames (the mmCIF version and>         the core>         CIF version) for each concept in core CIF has not caused confusion and extra work for the simple reason that there are clear>         workflow and software demarcations when doing macromolecular work and chemical crystallography. Programmers, being aware of this>         divide, work with the appropriate datanames. This demarcation is not a result of anything that COMCIFS have done and>         therefore the>         lack of confusion is not something that can be taken for granted when moving to a different community.>>         In contrast to the macromolecular/small molecule case, the modulated structures community and the magnetic structures>         community are>         closely intertwined to the extent that the same programs are used (e.g. JANA). Unlike the macromolecular/core CIF case, the>         program>         user does not in general know whether they are reading/writing a CIF intended for a modulated structures or a magnetic>         structures or>         plain core CIF consumer.  Therefore, if ms_cif is rewritten in DDL2, all programs must now be>         rewritten/recompiled/__redistributed to>         read and write both styles of datanames.  And what about the fact that many programs that ingest these magCIFs will be ordinary>         non-magnetic-aware programs expecting core CIF DDL1-style datanames for e.g. the atom positions?>>         A first cost benefit analysis then looks like this:>         Costs: rewriting 100 definitions and any software that inputs/outputs those datanames and core CIF datanames>         Benefits: all datanames in a loop can have dots in them>>         On the face of it, these costs outweigh the benefit by several orders of magnitude.>>         As a postscript, I don't know if we quite appreciate the fact that once we have defined a dataname, it is almost impossible to>         winkle it out of software.  Changing a dictionary from DDL1 style to dotted datanames has never been done before (I would assert>         that mmCIF started with a clean slate as their community path was PDB -> mmCIF, not core CIF -> mmCIF.  And it has only taken 15>         years to get /that/ to start to happen.)  The best I think we can do is to provide a solid and widely-adopted CIF API that>         can apply>>         aliases behind the scenes, in which case we can have a little more confidence in adoption of replacement datanames.>>         all the best,>         James.>>>>         On Wed, May 28, 2014 at 1:43 PM, Herbert J. Bernstein <yayahjb@gmail.com <mailto:yayahjb@gmail.com>>         <mailto:yayahjb@gmail.com <mailto:yayahjb@gmail.com>>> wrote:>>              Dear James,>>                 It need not cause any confusion.  The core names already in the mmCIF>              dictionary have not.  Small molecule people use the undotted names.>              Macromolecular people use the dotted names.  If we simply added aliases>              for the modulated structures to the mmCIF dictionary (which probably>              should be done anyway) we end up with nice clean magCIF loops and>              little or no confusion for modulated structure cifs.>>                 Regards,>                   Herbert>>>              On Tuesday, May 27, 2014, James Hester <jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>>         <mailto:jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>__>> wrote:>>                  I expect that the magCIF writers would write their datanames to match that part of mmCIF that reproduces core CIF.>           The only>                  issue then becomes the (DDL1) modulated structures dictionary. As you suggest, the modulated structures dictionary>         could be>                  rewritten with DDL2-style names, but I don't believe that this additional work is necessary.  It would also create>         unwelcome>                  confusion in the community as to which modulated structure datanames should be used.>>>                  On Tue, May 27, 2014 at 10:36 PM, Herbert J. Bernstein <yayahjb@gmail.com <mailto:yayahjb@gmail.com>> wrote:>>                      My own inclination would be to follow the approach followed by mmcif which provides a rather complete dotted>         notation>                      mapping of the core so you end up with much cleaner looking loop headers.>>                      Regards,>                      Herbert>>                      Sent from my Xperia™ smartphone>>>                      James Hester <jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>> wrote:>>                      Dear COMCIFS members and advisers:>>                      I am pleased to advise that a CIF dictionary for description of>                      magnetic structures (magCIF) is currently in preparation and it is>                      expected that a final draft could be ready before the IUCr meeting.>                      This has raised a policy issue for COMCIFS that we need to deal with>                      in a timely way.>>                      By its nature, the magCIF dictionary builds on the definitions in the>                      core CIF dictionary, modulated structures CIF dictionary, and symmetry>                      CIF dictionary (including extending looped categories).  At the same>                      time, the authors wish it to be a single, coherent document.  Core CIF>                      and the modulated structures dictionary use DDL1 naming conventions,>                      whereas symCIF is a DDL2 dictionary with DDL2 naming conventions. For>                      coherence and convenience, the authors of magCIF should clearly use a>                      single DDL and naming convention.>>                      My inclination is to recommend writing magCIF using DDL2.>                      Semantically, this will mean that certain DDL2 concepts (e.g. 'key')>                      will be implicitly imposed on DDL1 datanames.  This mapping is however>                      straightforward and implied by the presence of 'aliases' in mmCIF and>                      other DDL2 dictionaries>>                      More trivially, this approach will result in some loops that have>                      names not containing a period mixed with names that do contain a>                      period, and non-looped datanames in the CIF data file will also>                      contain mixtures of such names. I note that the use of a period to>                      separate category and item is purely conventional and is not>                      syntactically or semantically required by the DDL that the dictionary>                      is written in, so I do not consider this to be a problem.>>                      A further advantage of DDL2-style names is that when magCIF is>                      translated into DDLm at some not-too-distant point, the same names can>                      be used (as DDLm naming conventions are the same as DDL2 naming>                      conventions) and software written with the DDL2 magCIF dictionary in>                      mind will not require updating to handle files written against the>                      'new' DDLm magCIF.>>                      Does anybody see any issues with this recommendation?>>                      James.>>>                      -->                      T +61 (02) 9717 9907 <tel:%2B61%20%2802%29%209717%209907> <tel:%2B61%20%2802%29%209717%__209907>>                      F +61 (02) 9717 3145 <tel:%2B61%20%2802%29%209717%203145> <tel:%2B61%20%2802%29%209717%__203145>>                      M +61 (04) 0249 4148 <tel:%2B61%20%2804%29%200249%204148> <tel:%2B61%20%2804%29%200249%__204148>>>>                      _________________________________________________>                      comcifs mailing list>         comcifs@iucr.org <mailto:comcifs@iucr.org>>         http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>>>>>>                  -->                  T +61 (02) 9717 9907 <tel:%2B61%20%2802%29%209717%209907> <tel:%2B61%20%2802%29%209717%__209907>>                  F +61 (02) 9717 3145 <tel:%2B61%20%2802%29%209717%203145> <tel:%2B61%20%2802%29%209717%__203145>>                  M +61 (04) 0249 4148 <tel:%2B61%20%2804%29%200249%204148> <tel:%2B61%20%2804%29%200249%__204148>>>>              _________________________________________________>              comcifs mailing list>         comcifs@iucr.org <mailto:comcifs@iucr.org> <mailto:comcifs@iucr.org <mailto:comcifs@iucr.org>>>>         http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>>>>>>         -->         T +61 (02) 9717 9907 <tel:%2B61%20%2802%29%209717%209907>>         F +61 (02) 9717 3145 <tel:%2B61%20%2802%29%209717%203145>>         M +61 (04) 0249 4148 <tel:%2B61%20%2804%29%200249%204148>>>>         _________________________________________________>         comcifs mailing list>         comcifs@iucr.org <mailto:comcifs@iucr.org>>         http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>>>>     -->>     John Westbrook, Ph.D.>     RCSB, Protein Data Bank>     Rutgers, The State University of New Jersey>     Department of Chemistry and Chemical Biology>     174 Frelinghuysen Rd>     Piscataway, NJ 08854-8087>     e-mail: jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>>     Ph: (848) 445-4290 <tel:%28848%29%20445-4290> Fax: (732) 445-4320 <tel:%28732%29%20445-4320>>>     _________________________________________________>     comcifs mailing list>     comcifs@iucr.org <mailto:comcifs@iucr.org>>     http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>>>>>> --> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148
-- 
John Westbrook, Ph.D.RCSB, Protein Data BankRutgers, The State University of New JerseyDepartment of Chemistry and Chemical Biology174 Frelinghuysen RdPiscataway, NJ 08854-8087e-mail: jwest@rcsb.rutgers.eduPh: (848) 445-4290 Fax: (732) 445-4320_______________________________________________comcifs mailing listcomcifs@iucr.orghttp://mailman.iucr.org/mailman/listinfo/comcifs

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