New fast-track definition proposal: _diffrn_radiation_wavelength_nominal
David Brown
idbrown at mcmaster.ca
Tue Nov 3 21:20:19 GMT 2009
Variants is something we could consider for CIF2 in the future, but I
think we should learn to walk before we trying running. We don't even
have a syntax worked out yet, and until that is done I cannot start
converting the existing core dictionaries to CIF2. There will be enough
problems in this conversion without trying to add variants. The idea is
intriguing, but I don't imagine that users will rush to change their lab
procedures just so they can use coreCIF as a lab notebook - it will take
them some time just to come to terms with CIF2 as a repostiory of methods.
David
Herbert J. Bernstein wrote:
>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.
>
>save_VARIANT
> _category.description
>; 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
> list.
>
> 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
> _variant.timestamp.
>
> 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.
>
>;
> _category.id variant
> _category.mandatory_code no
> loop_
> _category_key.name '_variant.variant'
> '_variant.diffrn_id'
> '_variant.entry_id'
> loop_
> _category_group.id 'inclusive_group'
> loop_
> _category_examples.detail
> _category_examples.case
># - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>; 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.
>
>
>;
>;
>
> loop_
> _variant.variant
> _variant.role
> _variant.timestamp
> _variant.variant_of
> _variant.details
> . "raw data" 2007-08-03T23:20:00 . .
> indexed "preferred" 2007-08-04T01:17:28 .
> "indexed cell and refined beam center"
>
> loop_
> _diffrn_detector_element.detector_id
> _diffrn_detector_element.id
> _diffrn_detector_element.reference_center_fast
> _diffrn_detector_element.reference_center_slow
> _diffrn_detector_element.reference_center_units
> _diffrn_detector_element.variant
> 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
>;
># - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
> save_
>
>save__variant.details
> _item_description.description
>; A description of special aspects of the variant.
>;
> _item.name '_variant.details'
> _item.category_id variant
> _item.mandatory_code no
> _item_type.code text
> _item_examples.case
>; indexed cell and refined beam center
>;
> save_
>
>
>save__variant.role
> _item_description.description
>; The value of _variant.role specified a role
> for this variant. Possible roles are null, "preferred",
> "raw data", and "unsuccessful trial".
>;
> _item.name '_variant.role'
> _item.category_id variant
> _item.mandatory_code no
> _item_type.code uline
> loop_
> _item_enumeration.value
> _item_enumeration.detail
> .
>; 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.
>;
> "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.
>;
> save_
>
>
>save__variant.timestamp
> _item_description.description
>; 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.
>;
> _item.name '_variant.timestamp'
> _item.category_id variant
> _item.mandatory_code no
> _item_type.code yyyy-mm-dd
> save_
>
>
>save__variant.variant
> _item_description.description
>; The value of _variant.variant must uniquely identify
> each variant for the given diffraction experiment and/or
> entry
>
> This item has been made implicit and given a default value
> of null.
>;
> loop_
> _item.name
> _item.category_id
> _item.mandatory_code
> '_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
> implicit
> '_array_structure_list_axis.variant' array_structure_list_axis
> implicit
> '_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
> implicit
> '_diffrn_detector_element.variant' diffrn_detector_element
> implicit
> '_diffrn_measurement.variant' diffrn_measurement implicit
> '_diffrn_measurement_axis.variant' diffrn_measurement_axis
> implicit
> '_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
> implicit
> '_diffrn_scan_frame_monitor.variant' diffrn_scan_frame_monitor
> implicit
> '_map.variant' map implicit
> '_map_segment.variant' map_segment implicit
>
>
> _item_default.value .
> _item_type.code code
> loop_
> _item_linked.child_name
> _item_linked.parent_name
> '_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'
>
> save_
>
>
>save__variant.variant_of
> _item_description.description
>; 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.
>;
> _item.name '_variant.variant_of'
> _item.category_id variant
> _item.mandatory_code no
> _item_type.code code
> save_
>
>
>=====================================================
> 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 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
>>_______________________________________________
>>comcifs mailing list
>>comcifs at iucr.org
>>http://scripts.iucr.org/mailman/listinfo/comcifs
>>
>>
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