New fast-track definition proposal: _diffrn_radiation_wavelength_nominal

Herbert J. Bernstein yaya at
Tue Nov 3 03:24:33 GMT 2009

This comment is not intended to change the proposed minor fast track
change, but is a major change related to it that may be worth
discussing now.

The proposed change is a step in the right direction -- recognizing the 
subtle, but important variations in the experimental determinations of 
values such as wavelengths and cell parameters, as well as values 
provided by a delphic oracle.  In addition to the change 
proposed here, I would suggest considering the "_variant" tags we
are adding to the categories in the imgCIF dictionary, all of which
are based on a variant category.  This allows a CIF to be used as
a lab notebook while the final publication values are worked out.

;             Data items in the VARIANT category record
               the details about sets of variants of data items.

               There is sometimes a need to allow for multiple versions of
               the same data items in order to allow for refinements and
               corrections to earlier assumptions, observations and
               calculations.  In order to allow data sets to contain more
               than one variant of the same information, an optional
               ...variant data item as a pointer to _variant.variant has
               been added to the key of every category, as an implicit
               data item with a null (empty) default value.

               All rows in a category with the same variant value are
               considered to be related to one another and to all rows in
               other categories with the same variant value.  For a given
               variant, all such rows are also considered to be related to
               all rows with a null variant value, except that a row with a
               null variant value for which all other components of its
               key are identical to those entries in another row with a
               non-null variant value is not related to the rows with that
               non-null variant value.  This behavior is similar to the
               convention for identifying alternate conformers in an atom

               An optional role may be specified for a variant as the
               value of _variant.role.  Possible roles are null,
               "preferred", "raw data", "unsuccessful trial".

               Variants may carry an optional timestamp as the value of

               Variants may be related to other variants from which they
               were derived by the value of _variant.variant_of

               Further details about the variant may be specified as the
               value of _variant.details.

               In order to allow variant information from multiple datasets
               to be combined, _variant.diffrn_id and/or _variant.entry_id
               may be used.

;                   variant
     _category.mandatory_code       no
     loop_             '_variant.variant'
     loop_             'inclusive_group'
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
;   Example 1 - Distinguishing between a raw beam center and
        a refined beam center inferred after indexing.  Detector d1 is
        composed of four CCD detector elements, each 200 mm by 200 mm,
        arranged in a square, in the pattern

                    1     2
                    3     4

        Note that the beam centre is slightly displaced from each of the
        detector elements, just beyond the lower right corner of 1,
        the lower left corner of 2, the upper right corner of 3 and
        the upper left corner of 4.  For each element, the detector
        face coordiate system, is assumed to have the fast axis
        running from left to right and the slow axis running from
        top to bottom with the origin at the top left corner.

        After indexing and refinement, the center is shifted by .2 mm
        left and .1 mm down.


             . "raw data" 2007-08-03T23:20:00 . .
             indexed "preferred" 2007-08-04T01:17:28 .
               "indexed cell and refined beam center"

         d1     d1_ccd_1  201.5 201.5  mm  .
         d1     d1_ccd_2  -1.8  201.5  mm  .
         d1     d1_ccd_3  201.6  -1.4  mm  .
         d1     d1_ccd_4  -1.7   -1.5  mm  .
         d1     d1_ccd_1  201.3 201.6  mm  indexed
         d1     d1_ccd_2  -2.0  201.6  mm  indexed
         d1     d1_ccd_3  201.3  -1.5  mm  indexed
         d1     d1_ccd_4  -1.9   -1.6  mm  indexed
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -


;              A description of special aspects of the variant.
;                  '_variant.details'
     _item.category_id             variant
     _item.mandatory_code          no
     _item_type.code               text
;                                indexed cell and refined beam center

;             The value of _variant.role  specified a role
               for this variant.  Possible roles are null, "preferred",
               "raw data", and "unsuccessful trial".
;                  '_variant.role'
     _item.category_id            variant
     _item.mandatory_code         no
     _item_type.code              uline
;    A null value for _variant.role leaves the precise role of
      the variant unspecified.  No inference should be made that the
      variant with the latest time stamp is preferred.
;    A value of "preferred" indicates that rows of any categories
      specifying this variant should be used in preference to rows with the
      same key specifying other variants or the null variant.  It is an
      error to specify two variants that appear in the same category with
      the same key as being preferred, but it is not an error to specify
      more than one variant as preferred in other cases.
      "raw data"
;    A value of "raw data" indicates data prior to any corrections,
      calculations or refinements.  It is not necessarily an error for raw
      data to also be a variant of an earlier variant.  It may be
      replacement raw data for earlier data believed to be erroneous.
      "unsuccessful trial"
;    A value of "unsuccessful trial" indicates data that should not be
      used for further calculation.

;              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.timestamp'
     _item.category_id          variant
     _item.mandatory_code       no
     _item_type.code            yyyy-mm-dd

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

               This item has been made implicit and given a default value
               of null.
       '_variant.variant'                    variant             implicit
       '_variant.variant_of'                 variant             implicit
       '_array_data.variant'                 array_data          implicit
       '_array_element_size.variant'         array_element_size  implicit
       '_array_intensities.variant'          array_intensities   implicit
       '_array_structure.variant'            array_structure     implicit
       '_array_structure_list.variant'       array_structure_list
       '_array_structure_list_axis.variant'  array_structure_list_axis
       '_axis.variant'                       axis                implicit
       '_diffrn_data_frame.variant'          diffrn_data_frame   implicit
       '_diffrn_detector.variant'            diffrn_detector     implicit
       '_diffrn_detector_axis.variant'       diffrn_detector_axis
        '_diffrn_detector_element.variant'   diffrn_detector_element
        '_diffrn_measurement.variant'        diffrn_measurement  implicit
        '_diffrn_measurement_axis.variant'   diffrn_measurement_axis
        '_diffrn_radiation.variant'          diffrn_radiation   implicit
        '_diffrn_refln.variant'              diffrn_refln       implicit
        '_diffrn_scan.variant'               diffrn_scan        implicit
        '_diffrn_scan_axis.variant'          diffrn_scan_axis   implicit
        '_diffrn_scan_frame.variant'         diffrn_scan_frame  implicit
        '_diffrn_scan_frame_axis.variant'    diffrn_scan_frame_axis
        '_diffrn_scan_frame_monitor.variant' diffrn_scan_frame_monitor
        '_map.variant'                       map                implicit
        '_map_segment.variant'               map_segment        implicit

     _item_default.value           .
     _item_type.code               code
              '_array_data.variant'                 '_variant.variant'
              '_array_data.variant_of'              '_variant.variant'
              '_array_element_size.variant'         '_variant.variant'
              '_array_intensities.variant'          '_variant.variant'
              '_array_structure.variant'            '_variant.variant'
              '_array_structure_list.variant'       '_variant.variant'
              '_array_structure_list_axis.variant'  '_variant.variant'
              '_axis.variant'                       '_variant.variant'
              '_diffrn_data_frame.variant'          '_variant.variant'
              '_diffrn_detector.variant'            '_variant.variant'
              '_diffrn_detector_axis.variant'       '_variant.variant'
              '_diffrn_detector_element.variant'    '_variant.variant'
              '_diffrn_measurement.variant'         '_variant.variant'
              '_diffrn_measurement_axis.variant'    '_variant.variant'
              '_diffrn_radiation.variant'           '_variant.variant'
              '_diffrn_refln.variant'               '_variant.variant'
              '_diffrn_scan.variant'                '_variant.variant'
              '_diffrn_scan_axis.variant'           '_variant.variant'
              '_diffrn_scan_frame.variant'          '_variant.variant'
              '_diffrn_scan_frame_axis.variant'     '_variant.variant'
              '_diffrn_scan_frame_monitor.variant'  '_variant.variant'
              '_map.variant'                        '_variant.variant'
              '_map_segment.variant'                '_variant.variant'


;             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.

               This item is a pointer to _variant.variant in the
               VARIANT category.
;                  '_variant.variant_of'
     _item.category_id             variant
     _item.mandatory_code          no
     _item_type.code               code

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

                  yaya at

On Tue, 3 Nov 2009, James Hester wrote:

> Dear COMCIFS members: the following fast track proposal for a minor
> change to the coreCIF dictionary has been approved by the core
> Dictionary Maintenance Group after a 6-week comment period.  As per
> the recently approved fast track process, it is now open for comments
> from COMCIFS for a further 6 week period.
> James.
> ----------------------------------------------------------------------------------------------
> 2009-08-23 proposed by James Hester.
> 2009-10-16 approved by the core Dictionary Maintenance Group under a fast
>          track approval process.
> 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.
> ;
> -- 
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
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