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Re: comments on coreCIF.dic 2.1

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: comments on coreCIF.dic 2.1
  • From: "I. David Brown" <idbrown@mcmail.cis.McMaster.CA>
  • Date: Thu, 21 Jan 1999 14:52:57 GMT
Here are my comments on recent comments.


On Wed, 20 Jan 1999, Howard Flack wrote:

> >10. _diffrn_radiation_polarisn_norm
> >11. _diffrn_radiation_polarisn_ratio
>   The definitions are bad or incomplete, I am very well prepared to
> admit but both need input from people that have need of them now. In
> order to allow Brian to finish this release, I suggest that we leave
> them as such at the moment and ask the experts (during the Glasgow
> congress) what they really need and how they do things.


> > (17)  data_refln_symmetry_multiplicity
> >        The Fs may be different but their MAGNITUDES (as mentioned in the
> > definition) are the same if one ignores the imaginary components of the
> > scattering factors.
>   The general, and nowadays usual, case is that the imaginary component
> is significant, even if small. That is the one I always have in mind.
> Vanishingly small f''s are a special case.
> >   I think some clarification is needed in the case of
> >   non-centrosymmetric structures,
>   Yes I agree. The mention of structure-factor magnitudes as a criterion
> makes things very murky indeed.  The criterion must be only one of
> symmetry. I would write the existing definition as follows:
> Definition L:    The number of reflections symmetry-equivalent under the
> Laue symmetry
>                  to the present reflection. In the Laue symmetry, 
>                  Friedel opposites (h k l and -h -k -l) are equivalent.
> Tables of
>                  symmetry-equivalent reflections are available in
> International Tables
>                  for Crystallography, Volume A, section 10.2 .
>   This mentions the Laue symmetry in which Friedel opposites are
> equivalent. A definition of something related would be:
> Definition C:    The number of reflections symmetry-equivalent under the
> crystal point
>                  group to the present reflection. Only in
> centrosymmetric point 
>                  groups are the Friedel opposites (h k l and -h -k -l)
> equivalent.
>                  Tables of symmetry-equivalent reflections are available
> in 
>                  International Tables for Crystallography, Volume A,
> section 10.2 .
>   This uses the crystal point group. The two values (L and C) are
> identical in the case of a centrosymmetric structure.
>   As in pure mathematical form, the count includes the basic reflection
> because it is always equivalent to itself.
>   If both of these definitions are useful, they would need to be given
> separate names. 
>   Conclusion: The existing definition of _refln_symmetry_multiplicity is
> confusing but it needs input all round to find something useful to
> correct it.

Since, if this information is needed, two different data names are needed
corresponding to L and C above, I suggest we use the current data name for
L, since this definition corresponds most closely to the existing
definition.  We might tighten it up by adopting Howard's wording for L.
If anyone needs C as well we will have to find a new and different
dataname to which we could attach Howard's C definition, but I see no

> > >13. _diffrn_refln_intensity_sigma
> > >    _diffrn_reflns_av_sigmaI/netI
> > >    _diffrn_reflns_class_av_sgI/I
> > >    _diffrn_standards_scale_sigma
> > >    _refine_ls_weighting_scheme 
> > >    _reflns_threshold_expression
> > >    _reflns_shell_meanI_over_sigI_ (two data items)
>   It seems to me that there is no implicit or explicit requirement in
> any of the above definitions that the uncertainties there referenced
> should contain only contributions estimated from the Poisson counting
> statistics. I always understood these uncertainties to be much more
> general and capable of including whatever one thought wise and expedient
> to put there. I do not think that there is any specific data item in
> which one can describe how e.g. _diffrn_refln_intensity_sigma is
> calculated. For us it defintely includes contributions from the
> uncertainties of the attenuator, the scales, the stability etc and is
> never pure Poisson.
>   The agreed symbol for standard uncertainty is u.  So:
>      _diffrn_refln_intensity_u
>      _diffrn_reflns_av_unetI/netI
>      _diffrn_reflns_class_av_uI/I
>      _diffrn_standards_scale_u
>      _reflns_shell_meanI_over_uI_ (two data items)
>     would be fine for me. I expect that there are other sigma, sig, sg,
> etc in the core dictionary. 


From: Gotzon Madariaga <wmpmameg@lg.ehu.es>

I agree with all of Gotzon's suggestions except as follows.

> 1. _atom_site_aniso_B_
> an _enumeration_range of 0: should be added to this item, according to
> further definitions like _atom-site_B_equiv_geom_mean and
> _atom_site_B_iso_or_equiv

While I agree in general with the idea of adding the various enumeration
ranges suggested by Gotzon, I am more hesitant in this case.  While it is
true that negative B's have no physical significance, they not
infrequently appear during refinement.  When they do appear, they are an
important diagnostic indicating problems in the refinement.  I can imagine
cases where a negative B or U might be reported to indicate to a colleague
or editor the nature of the problem.  I would recommend not specifying an
enumeration range here.   One could add a note that negative values have
no physical significance, but I do not think this is necessary.

> 8. Should _diffrn_measured_fraction_theta_ items appear in list?. If yes
> a _list_reference should be given (_diffrn_crystal_id ?). As far as I
> understand, if several crystals are used and their intensities are
> intended to be merged (case of unstable crystal for instance) only these
> two items should be looped.

My understanding is that this item is designed to refer to the whole set
of intensity measurements after sets from different crystals have been
merged.  The item was designed to meet the need of Acta Cryst to assess
the extent of the coverage of reciprocal space used in a refinement.  If
it is necessary to break the measurements down by different crystals
(which is not common for small unit cell work), then we should have a
_diffrn_crystal category.  But I do not see a need for that at the moment.

> 9. _diffrn_radiation_detector and _diffrn_radiation_detector_dtime are
> not in the correct category.

These are obsolete datanames kept here for backward compatibility.  This
is clear in the printed copy where they appear in bold type.  They are in
the correct category, or at least they are listed under the category where
they should appear.  There were some new categories introduced in version
2 when these names became obsolete and I do not have any information about
the category they were in in version 1

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