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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: Tue, 19 Jan 1999 14:16:48 GMT
	Some of Howard's comments seem to require a response from me.  I
will try to be brief.

				David

Keep on scrolling - more below
*****************************************************
Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research, 
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************

> 
> >10. _diffrn_radiation_polarisn_norm
> >      'perpendicular component of the polarisation' is rather
> >meaningless.  I assume what is meant is the 'electric vector of the
> >major component of the polarisation'.
>    

	Thanks, Howard, for your very clear explanation of what is meant
(which for brevity I have deleted from this message).  The fact that I was
unable to interpret the definition must surely indicate a weakness.  At
the very least it would seem a reference to Azaroff should have been
given.  What about adding the following to the existing definition: 

'The perpendicular component of the radiation is the component
perpendicular to the reflecting plane, i.e., the component that lies in
the diffraction plane. [We should add a reference to Azaroff]'

	If I have interpreted Howard correctly this should be the
complement of the Bragg angle - or have I missed something?

> >11. _diffrn_radiation_polarisn_ratio
> >      This is quite a confusing definition.  I assume that what is
> >meant is: 'The ratio of the intensities of the major polarisation
> >component to the component perpendicular to this.  The direction of
> >the electric vector of the major component is given in _*_norm.'

>    It seems to me that one needs advice from people using CIF and
> synchrotron radiation before playing around with these definitions.

	I am willing to wait for this advice.  This does not prevent
making a clarification in the _*_norm definition, however.

> 
> 
> >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)
> >      There is an element of confusion in these data definitions. 
> > We have replaced the ambiguous e.s.d. by s.u.
> 
>    I do not agree with David's interpretation.
>    sigma should be reserved for the square root of the variance of a
> probability density function. It is a theoretical value, unknowable and
> unmeasurable.
>    (Standard) uncertainties are experimentally-determined values, or
> values taken from prior information, or a combination of the two.
>    Indeed experimental values in CIF should not mention sigma or sigmaI
> or sigI or sgI (especially in such variety) but should only use some
> uniform way of abreviating 'standard uncertainty' in the text and in the
> data names. Hardly surprisingly the last time I suggested this there was
> very little enthusiasm for its implementation.

	I am all with Howard for trying to clean this up [signs of
enthusiasm :-)].  However, the fact remains that crystallographers make
extensive use of the contribution to the standard uncertainty derived from
counting statistics alone, which is not to be confused with the true
standard uncertainty usually calculated with the aid of an expression that
involves both the counting statistics and the structure factors.  Much of
what is carried through from the experiment is just the counting
statistics uncertainty (c.s.u.)  and the final estimate of the s.u. is
only made during the refinement.  It is incorrect to call the c.s.u. the
standard uncertainty.  Surely we need to make this distinction clear and
recognise that most of these terms, particularly in the _diffrn
categories, are c.s.u.'s, not s.u.'s.  If Howard does not like 'sigma' to
describe c.s.u. would he like to suggest a better name and abbreviation? 

> 
> (3) data_diffrn_measured_fraction_theta_full
>     Should not    _enumeration_range    0:1.0 really be 0.95:1.0 since 
> _diffrn_reflns_theta_full mentions 'nearly complete'. 0.0 or 0.5 do not
> seem 'nearly complete' to me!?

I agree with Brian here that the dictionary definitions should reflect
what is possible, not what is desirable. 

> 
> (4) data_diffrn_refln_[]
>     I suggest either adding parentheses in the definition or omitting
> the part that I have now put in parentheses:
>
>     _definition
> ;              Data items in the DIFFRN_REFLN category record details
> about
>                the intensities measured in the diffraction experiment.
> 
>                The DIFFRN_REFLN data items refer to individual intensity
>                measurements, and must be included in looped lists.
> 
>                (The DIFFRN_REFLNS data items specify the parameters that
> apply
>                to all intensity  measurements. The DIFFRN_REFLNS data
> items
>                are not looped.)
> ;

	This section should not be deleted since a novice will be quite
confused by the distinction we make between 'refln' and 'reflns' and will
probably not even notice the difference unless it is pointed out.  By all
means add parentheses.

> 
> (6)  data_diffrn_reflns_[]

	Same as above.

 
> 
> (17)  data_refln_symmetry_multiplicity
>      In the definition remove ' and the Friedel relationship' to give:
>     _definition
> ;              The number of symmetry-equivalent reflections. The
> equivalent
>                reflections have the same structure-factor magnitudes
> because
>                of the space-group symmetry.
> ;
>      There is no case for adding in a centre of symmetry. h k l and -h
> -k -l do not have the same Fs in a non-centrosymmetric space group.

	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.  I think some clarification is needed in the case of
non-centrosymmetric structures, such as the removal of the word
'magnitude' from the definition, or a explanation of when h k l and -h -k
-l are deemed not to be equivalent.

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