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
[email protected]
=====================================================
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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