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Re: magCIF - policy advice requested

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.


On Tuesday, May 27, 2014, James Hester <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.


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?


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