Re: CIF/PDB reflection file format (crosspost from PDB mailing list)

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On Thu, 16 Nov 1995, Murray-Rust Dr P wrote:

> On Thu, 9 Nov 1995, robert w harrison wrote:
> 
> > There are two issues in CIF.  
> 
> I am on the COMCIFs mailing list and although I can't speak for that 
> group I hope I can  help a bit.  Although I appreciate your frustration 
> this is a MUCH more difficult problem than most people realise and I 
> think the crystallogarphic community has made great progress.

Yes, I agree with all of that.

> > The Star language is probably not optimal
> > and is the cause of much of the problems.  
> > Formally it is context-dependant (you
> 
> CIF is NOT  context-dependent - it IS representable by a BNF.  I thought 
> this was also true for STAR.

Yes, of course it is. There are one or two problems with the details at 
the moment, but hopefully they will be straightened out shortly.

> One of the issues I have been trrying to resolve in CIF is the 
> distinction between syntax and semantics.  In simple terms syntax means 
> parsing the file without attempting to interpret its meaning or content.  
> In general CIF (note that the core CIF dictionary does not use the full 
> STAR language) has a well-defined syntax and can be expressed by a BNF.  
> There are - I think - still a few concerns such as how to escape certain 
> characters and what to do when 'including' files.  

As far as mmCIF is concerned, it is possible to separate the two by 
treating the subset of STAR which is allowed in CIF's, as specifying the 
syntactical and lexical aspects, with the dictionary (and indirectly the 
Dicationary Definition Language) providing the semantics. (This may not 
be true of the core CIF dictionary - I'm not so familiar with that.)

> Semantics determines what meaning you put on the contents.  For example,
> 
> _cell_length_a_pm  1490.3

This unit extension business is a real problem for mmCIF at the moment.
Fortunately, it is relatively easily correctable, and I will be submitting a
proposal to do just that later today or tomorrow (thanks, Peter, for
reminding me that this needed dealing with!). I will be sending it to the
mmDDL mailing list - those of you who are interested in this kind of 
thing, should join that list: 

   To: requests@ndbserver.rutgers.edu

   subscribe mmddlnews "Name Surname"
   
or check the mailing list in a couple of days (on
http://ndbserver.rutgers.edu/DDL/index.html, although their server seems to
be down at the moment). In fact, this whole discussion really belongs on the
DDL mailing list anyway - I'm posting this message there as well, and I would
suggest that followups go there too. 

Regards,
Peter.

P.S. Don't forget about the mmCIF mailing list as well - details on 
http://ndbserver.rutgers.edu/mmcif/index.html .

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Peter Keller.            \ 
Dept. of Biology and      \ "It is a pity that people are being killed
    Biochemistry,          \  by my guns"
University of Bath,         \ 
Bath, BA2 7AY, UK.           \          --- Mikhail Kalashnikov
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