Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: DDL2/mm_CIF bugs/suggestions

James

Timing...

Volume G has just gone to press; copies will be available at the
Florence Congress so long as there are no disasters at the printers.

Volume G represents the "official" view at this time of currency of
dictionaries and specifications. The current version of the mmCIF
dictionary is labelled 2.0.09; the current "official" DDL2 version
is 2.1.3 (since that is discussed at length in the commentary chapters),
although there is a 2.1.6 available from the mmcif.pdb.org site, and 
that is what is actively used by the RCSB in developing the mmCIF
and related dictionaries.

I'll make a formal announcement about the canonical dictionaries
later this week when I've had time to update the IUCr web pages
(all have been revised for Volume G, though in many cases the
revisions are minor rewordings of text definitions).

If anyone is too keen to await that announcement, the CIF dictionary
register ftp://ftp.iucr.org/pub/cifdics/cifdic.register will give you
the URLs of all the latest versions.

> I found this by trying to validate cif_mm_2.0.03.dic against ddl2.c96 -
> surely this is not the first time that this has been attempted??

So I'd be grateful if you would try validating mmcif_std.dic version
2.0.09 against ddl_core_2.1.3.dic and then against mmcif_ddl_2.1.6.dic   
(with apologies for the vagaries of the naming scheme).


While I'm here...
 
> 4. If people are serious about using the cif_mm dictionary to validate
> files supported by cif_core, I would suggest some sort of mechanism to
> indicate when a dataname first appeared in the aliased dictionary (e.g.
> _item_aliases.version_first) rather than simply giving the version in
> which the dataname appears.  As currently set up, the cif_mm dictionary
> will have to carry around a long list of aliases for each dataname, with
> one entry for every version of cif_core containing that dataname.

Some of us have had informal discussions about this issue, and my current
understanding is that the intention is that the alias tracks the earliest
version of the dictionary in which the aliased name was introduced (the idea
being that a data name introduced to version 1 will still be found in
version 2 and later; conversely, if the latest version of the dictionary
referred to is version 3 and that is fetched, it will contain all the
aliases that were introduced in versions 1, 2 etc).

This has not been formalised - but of course should be, at some stage.
However, this provides an opportunity for the community to discuss whether
the convention described above is workable and appropriate.

Best wishes
Brian
_______________________________________________
cif-developers mailing list
cif-developers@iucr.org
http://scripts.iucr.org/mailman/listinfo/cif-developers

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Council for Science (admitted 1947). Member of CODATA, the ICSU Committee on Data. Member of ICSTI, the International Council for Scientific and Technical Information. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

ICSU Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.