[Fwd: Re: New fast-track definition proposal: _diffrn_radiation_wavelength_nominal]
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Wed Nov 25 21:44:13 GMT 2009
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 at 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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