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Re: magCIF - policy advice requested

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.



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>> 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>> 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> 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> 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.
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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
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