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Re: Core CIF - revision to accommodate Acta C Notes for Authors

  • To: COMCIFS@iucr
  • Subject: Re: Core CIF - revision to accommodate Acta C Notes for Authors
  • From: Brian McMahon <bm@iucr.org>
  • Date: Mon Nov 24 15:27:23 1997
  • In-Reply-To: <000000001@iucr.org>
D> 	A quick look through the proposed core changes raises the
D> following queries and comments:
D> *_obs
D> 	These items are all referenced to *_gt.  Since we have decided to
D> go for *_gt, why are we now introducing *_obs items for the first time? 
D> Surely it is bad enough to build in obsolescence without actually
D> introducing data names that are already obsolete before they are defined! 
D> (Does 'obs' stand for obsolete? :).  The same comment applies to
D> *_shift/esd_*. 

The reference is through the DDL1.4 terms "_related_item" and
"_related_purpose  replace". These are added to the *old* item, not the new
one. Although this may seem counter-intuitive, the idea is that a CIF reader
working through archival data will be pointed forward to the definition that
supersedes the older one. DDL2 has a better bidirectional formalism, where
the related functions are "replaces" and "replacedby", and I think this
would be an improvement that one might consider for DDL version 1.5. No new
'obs' terms have been introduced.

D> _refine_ls_wR_factor_gt
D> 	We discussed the definitions of R factors some time ago and I
D> thought we had decided that there was only one possible definition of wR,
D> namely what here is called *_wR_factor_ref.  Any omitted reflections are
D> those in which w is set equal to zero, so, since w is presumably defined
D> for each reflection, *_wR_factor_gt is a nonsense and should not be
D> allowed into the dictionary (this would also exclude *_obs).  If it is
D> absolutely essential to include this definition for historical reasons, is
D> there anyway we can point out its mathematical absurdity and
D> inappropriateness for any valid crystallographic purpose? 

There are many instances of *_obs in the Acta archive. The *_gt form was
introduced solely to yield a parallel translation to the other *_obs->*_gt
changes. I am willing to entertain the idea that we do not introduce the
*_gt form, but instead add to *_obs the entries
    _related_item     '_refine_ls_wR_factor_ref'
    _related_purpose    replace
as a pointer to (database querying) software to consider the *_ref name as a
replacement for *_obs (though the definitions are in fact slightly
different). Are there any objections to this?

D> _refine_ls_shift/su_mean
D> 	The related item I assume should be *_shift/esd_mean, not
D> *_shift/su_mean.

I've deleted the "_related_item" entry altogether in this case.

D> _reflns_number_Friedel
D> 	The last line of the definition should read 'anomalous scattering'
D> not 'inelastic scattering'.

OK, I've made that change. 

D> _reflns_threshold_expression
D> 	Would it be better to say 'USUALLY based on multiples of' or
D> 'based on FUNCTIONS of'?  I do not see any need to restrict the nature of
D> the function being defined in such a drastic way, even if it does cover
D> 99% of current usage.

;              The threshold, usually based on multiples of \s(I), \s(F^2^)
               or \s(F), that serves to identify significantly intense
               reflections, the number of which is given by _reflns_number_gt.
               These reflections are used in the calculation of

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