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RE: [Fwd: Re: New fast-track definitionproposal:_diffrn_radiation_wavelength_nominal]

  • To: "Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group" <coredmg@iucr.org>, "Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group" <coredmg@iucr.org>
  • Subject: RE: [Fwd: Re: New fast-track definitionproposal:_diffrn_radiation_wavelength_nominal]
  • From: "Haltiwanger, Curtis" <chaltiwa@cephalon.com>
  • Date: Thu, 26 Nov 2009 12:57:31 -0500
  • References: <4B0D90EC.1090102@mcmaster.ca><alpine.BSF.2.00.0911251616450.44405@epsilon.pair.com>

As I said I have only used lab sources, so I have not needed other wavelengths.
That makes it hard for me to comment on this further extension.  
In general, I like including additional information.  
Probably because of my lack of experiance thsi extension seems complicated to me. 
I'll leave it to others to comment and evaluate.

R. Curtis Haltiwanger
Research Scientist
Cephalon, Inc.

-----Original Message-----
From: coredmg-bounces@iucr.org on behalf of Herbert J. Bernstein
Sent: Wed 11/25/2009 4:44 PM
To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group
Subject: Re: [Fwd: Re: New fast-track definition proposal:_diffrn_radiation_wavelength_nominal]
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


you would add


and a new variant category


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:


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


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


               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.


               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.


               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

                  final   1.23456
                  pelim   1.25
               final preferred 2007-08-04T01:17:28 prelim refined
               prelim .        2007-08-03T23:20:00 . .

              final  22.5 22.5 22.5 90. 90. 90.
              prelim 22.3 22.3 22.3 90. 90. 90.


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


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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