Section 3.2.2.2.5. Intensity measurements

The data items in these categories are as follows:

(a) DIFFRN_REFLN

(b) DIFFRN_REFLNS

(c) DIFFRN_REFLNS_CLASS

(d) DIFFRN_SCALE_GROUP

(e) DIFFRN_STANDARD_REFLN

(f) DIFFRN_STANDARDS

The bullet () indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow () is a reference to a parent data item. The dagger () indicates a deprecated item, which should not be used in the creation of new CIFs.

The DIFFRN_REFLN category describes the measured reflections in a diffraction experiment. Example 3.2.2.3 shows a listing from a CAD-4 single-crystal diffractometer.

Note that the data in this list refer to the raw measurements as acquired at the time of data collection. This is in contrast to the data in the REFLN list, which refer to the reflections after merging and scaling.

The meanings of most of the data names can be deduced by inspection of this example. Full definitions are given in the dictionary.

However, the category also contains a number of data items which are used to group blocks of reflections with additional properties described by data items in other categories. For example, a number of reflections in the list might share a common value of _diffrn_refln_scale_group_code; this value would link to a description in the DIFFRN_SCALE_GROUP category of the scaling factor that needs to be applied to this group of reflections to bring all intensities in the list on to a common scale. (For example, intensities might be obtained from individual films in a multi-film data set or from a number of separate crystals.)

Likewise, individual reflections might be marked to indicate that they were monitored as standards during the course of the experiment, using the data name _diffrn_refln_standard_code. These standard reflections may be listed separately in the DIFFRN_STANDARD_REFLN category, in which case they are labelled by _diffrn_standard_refln_code, which must have values matching those assigned in the main list of intensities.

Apart from these specific classes of reflections, the intensity data may be binned according to different criteria (e.g. for modulated structures the intensities are often partitioned into classes with the same value of , where the are the integer coefficients indexing diffraction vectors in an n-dimensional representation). The data name _diffrn_refln_class_code is provided as a link to the different classes of reflections defined in the DIFFRN_REFLNS_CLASS category.

The DIFFRN_REFLNS category describes collective properties of the set of experimental intensity measurements and follows the convention (common elsewhere in the dictionary) of having a name very similar to the related DIFFRN_REFLN category, but using a plural form of the relevant term in the composite name. While the individual DIFFRN_REFLN entries appear in a looped list, the items in the DIFFRN_REFLNS category are not looped.

This category describes properties of the complete measurement set; descriptions of specific portions of the complete set are handled by the DIFFRN_REFLNS_CLASS category.

Several of the items that appear in this category can be derived from the contents of the DIFFRN_REFLN lists, but it is often convenient to list them separately for ease of access and as a consistency check.

Note the definition of _diffrn_reflns_number as the total number of measured intensities excluding those classed as `systematically absent' (reflections whose intensities are null as a consequence of crystallographic symmetry). There is no data item to specifically flag systematic absences (although one could assign a distinct _diffrn_refln_class_code value and define the relevant DIFFRN_REFLNS_CLASS). Because the measured diffraction data may (and often do) include reduced measurements and symmetry-equivalent reflection intensities, there is no formal way to check the value of _diffrn_reflns_number with dictionary-driven validation software. (Note that systematic absences are flagged in the structure-factor listing of the REFLN category.)

The data items in the DIFFRN_REFLNS_CLASS category record details about classes of reflections measured in the diffraction experiment. The user is free to assign classes according to arbitrary criteria; two specific cases, the marking of standard reflections and the clustering of intensities that need to be scaled by a common factor, have their own specific data items and associated categories, as discussed above. The example given in the dictionary (Example 3.2.2.4) describes a one-dimensional incommensurately modulated structure, where each reflection class is defined by the number , where the are the integer coefficients that, in addition to h, k, l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice.

The DIFFRN_SCALE_GROUP category records scaling factors which must be applied to specific intensities in the DIFFRN_REFLN list to bring all the measurements on to a common scale (Example 3.2.2.5). The scale factor _diffrn_scale_group_I_net is the factor by which the relevant net values in the intensities list must be multiplied. The intensities to which it must be applied are those in the intensities list marked with a _diffrn_refln_scale_group_code that matches the corresponding _diffrn_scale_group_code in this category.

The DIFFRN_STANDARD_REFLN category allows a separate tabulation of the reflections used as standards. Note that the actual measurements on these reflections are stored alongside all the other measurements in the DIFFRN_REFLN list. The results of the analysis of the standard reflections are described by the DIFFRN_STANDARDS category.

The DIFFRN_STANDARDS category describes the interval between measurements of the standard reflections and their overall intensity change (usually a decay, so that the relevant data name is _diffrn_standards_decay_%; this data item has a negative value if the final measured intensities are greater than the initial ones). The items assume a constant time interval (or number of counts) between the measurement of each standard and a single global value for the overall intensity change. If required, detailed tracking of the intensity change of individual standard reflections can be extracted from the DIFFRN_REFLN list provided the elapsed time at each measurement has been recorded ( _diffrn_refln_elapsed_time).