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Re: [Fwd: Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal]

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Re: [Fwd: Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal]
  • From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
  • Date: Wed, 25 Nov 2009 16:44:13 -0500 (EST)
  • In-Reply-To: <4B0D90EC.1090102@mcmaster.ca>
  • References: <4B0D90EC.1090102@mcmaster.ca>
Dear Colleagues,

   While you are revisiting this item, I would suggest you consider the 
more complete (and, I believe, more elegant and general) solution of 
defining "variants", that we have introduced into the imgCIF dictionary to 
handled quantities that may be determined in different ways.

   Instead of adding

   _diffrn_radiation_wavelength_determination

you would add

   _diffrn_radiation_wavelength_variant

and a new variant category

         _variant_variant
         _variant_role
         _variant_timestamp
         _variant_variant_of
         _variant_details

which would allow you with complete generality to manage any number
a refined or redefined quantities, such as wavelengths.  This would
then allow you to us the same variant identifier, for, say cell
dimensions, which could be expected to change in a coupled manner
with the changes in wavelength.

   If you are interested in this more complete approach, I can provide
you with the full item definitions, but the short form is:

         _variant_variant

               The value of _variant_variant must uniquely identify
               each variant for the given diffraction experiment and/or
               entry

         _variant_role

               The value of _variant_role  specifies a role
               for this variant.  Possible roles are null, "preferred",
               "raw data", and "unsuccessful trial".

         _variant_timestamp

               The date and time identifying a variant.  This is not
               necessarily the precise time of the measurement or
               calculation of the individual related data items, but a timestamp that
               reflects the order in which the variants were defined.

         _variant_variant_of

               The value of _variant.variant_of gives the variant
               from which this variant was derived.  If this value is not
               given, the variant is assumed to be derived from the default
               null variant.

         _variant_details

               A description of special aspects of the variant


> An example of how this might be used is:
>
>          loop_
>              _diffrn_radiation_wavelength_id
>              _diffrn_radiation_wavelength
>              _diffrn_radiation_wavelength_determinaton
>                 1   1.23456   fundamental
>                 2   1.25      estimated


would become

           loop_
               _diffrn_radiation_wavelength_variant
               _diffrn_radiation_wavelength
                  final   1.23456
                  pelim   1.25
           loop_
               _variant_variant
               _variant_role
               _variant_timestamp
               _variant_variant_of
               _variant_details
               final preferred 2007-08-04T01:17:28 prelim refined
               prelim .        2007-08-03T23:20:00 . .

           loop_
              _cell_variant
              _cell_length_a
              _cell_length_b
              _cell_length_c
              _cell_angle_alpha
              _cell_angle_beta
              _cell_angle_gamma
              final  22.5 22.5 22.5 90. 90. 90.
              prelim 22.3 22.3 22.3 90. 90. 90.


   Regards,
     Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
=====================================================

On Wed, 25 Nov 2009, David Brown wrote:

> Dear Colleagues,
> 
> Last September I circulated for fast track approvel a recommendation for adding a
> new item:                             
> 
>                  _diffrn_radiation_wavelength_nominal,
> 
> to the core dictionary (see below for details).  The intent was that this could be
> used for giving a nominal wavelength calculated e.g., from the paparmeters of a
> diffractometer.  It was proposed tht this might be needed for completeness even
> though it was not accurate enough for calculating  lattice parameters, etc.  This
> proposal was passed by the core CIR dictionary maintenance group by default (no
> one raised any objection).  When this proposal was subsequently presented for
> final approval to COMCIFS, Nick Spadaccini suggested a more elegant alternative,
> namely that by adding instead the item
> 
>         _diffrn_radiation_wavelength_determination 
> 
> we could loop the nomiinal wavelength with the  refined (and any other
> interesting) wavelengths.  This would be more informative and allow for future
> expansion.
> 
> An example of how this might be used is:
> 
>          loop_
>              _diffrn_radiation_wavelength_id
>              _diffrn_radiation_wavelength
>              _diffrn_radiation_wavelength_determinaton
>                 1   1.23456   fundamental
>                 2   1.25      estimated
> 
> According to our rules, this proposal is being posted for comment to the coreCIF
> dictionary maintenance group for the next six weeks.  At the end of this time, if
> there are no unresolved issues, the core dictionary maintenance group will be
> deemed to have accepted the proposal.
> 
> David Brown
> 
> ==============================================================
> 
> The proposal is to add the following item to the coreCIF dictionary:
> =============================================
> 
> 2009-09-25 Proposal from the Nick Spadaccini on the COMCIFS dicsussion list to
> replace a withdrawn proposal.
> 
> data_diffrn_radiation_wavelength_determination
>   _name                      '_diffrn_radiation_wavelength_determination'
>   _category                    diffrn_radiation_wavelength
>   _type                        char
>   _list                        both
>   _list_reference            '_diffrn_radiation_wavelength_id'
>  loop_
>    _enumeration
>    _enumeration_detail
>   'fundamental'           
>        'Wavelength that is a fundamental property of matter e.g. MoK\alpha'
>   'estimated'               
>        'Estimated from secondary information e.g. monochromator angle or time of
> flight'
>   'refined'                 
>        'Based on refinement using a standard material with known cell parameters'
> 
>   _definition
> ;              The method of determination of incident wavelength. Further
> information may be provided in _diffrn_radiation_special_details
> ;
> 
> 
> The original proposal was as follows:
> =========================
> >>
> >> 2009-08-23 proposed by James Hester.
> >> 2009-10-16 approved by the core Dictionary Maintenance Group under a fast
> >>           track approval process.
> > > 2009-11-25 proposal withdrawn in favour of  an alternative
> >>
> >> Explanation
> >> ===========
> >> The wavelength used for a measurement defines the
> >>  length scales used in the crystallographic unit cell, so it is
> >>  important that the quality of the number used for wavelength is
> >>  understood.  When the bulk of experiments came from lab X-ray sources,
> >>  the wavelength value was an accurate and precise quantity that could
> >>  be relied on.  In contrast, synchrotron and neutron sources have
> >>  comparatively poorly-defined wavelengths, subject to systematic errors
> >>  (for example, changes in the monochromator d-spacing due to
> >>  temperature effects, and angular offset errors).  Many facilities do
> >>  not attempt to characterise the accuracy of such derived wavelength
> >>  values. Instead users may (or may not) refine against a standard
> >>  compound in order to recover an accurate wavelength value. I therefore
> >>  propose a separate tag for those wavelength values that are nominal,
> >>  that is, derived from positioning of optical elements rather than
> >>  proper standards.  This removes ambiguity in determining whether or
> >>  not a wavelength has been obtained from refinement against a standard,
> >>  or is simply a nominal value based on beamline optics.
> >>
> >>
> >> A new DDL1 item
> >>
> >>  data_diffrn_radiation_wavelength_nominal
> >>     _name                      '_diffrn_radiation_wavelength_nominal'
> >>     _category                    diffrn_radiation_wavelength
> >>     _type                        numb
> >>     _list                        both
> >>     _list_reference            '_diffrn_radiation_wavelength_id'
> >>      _enumeration_range           0.0:
> >>     _units                       A
> >>     _units_detail              'angstroms'
> >>     _definition
> >> ;              The incident radiation wavelength in Angstroms
> >>               calculated from secondary information,
> >>               for example monochromator angle or time of flight.
> >>               If the wavelength has been determined
> >>               using some type of standard,
> >>               _diffrn_radiation_wavelength should be used
> >> ;
> >>
> >> A change in definition of an existing item.  The current
> >> definition reads 'The radiation wavelength in angstroms'.
> >>
> >>
> >>  data_diffrn_radiation_wavelength
> >>     _name                      '_diffrn_radiation_wavelength'
> >>     _category                    diffrn_radiation_wavelength
> >>     _type                        numb
> >>     _list                        both
> >>     _list_reference            '_diffrn_radiation_wavelength_id'
> >>     _enumeration_range           0.0:
> >>     _units                       A
> >>     _units_detail              'angstroms'
> >>     _definition
> >> ;              The radiation wavelength in angstroms as
> >>               determined from measurements using standards,
> >>               for example an X-ray emission line,
> >>               or when a refinement based on a standard
> >>               material has been carried out.
> >>               The details of such a refinement should be
> >>               recorded in the _diffrn_radiation_special_details
> >>               item.
> >>  ;
> 
> 
>  
> 
> 
>
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