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Re: New fast-track definitionproposal: _diffrn_radiation_wavelength_nominal
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: Re: New fast-track definitionproposal: _diffrn_radiation_wavelength_nominal
- From: David Brown <idbrown@mcmaster.ca>
- Date: Tue, 03 Nov 2009 16:20:19 -0500
- In-Reply-To: <20091102215349.U83410@epsilon.pair.com>
- References: <279aad2a0911021852q329a5eej75d5754548218476@mail.gmail.com><20091102215349.U83410@epsilon.pair.com>
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@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@iucr.org http://scripts.iucr.org/mailman/listinfo/comcifs_______________________________________________ comcifs mailing list comcifs@iucr.org http://scripts.iucr.org/mailman/listinfo/comcifs |
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