International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.7, pp. 202-205

Section 3.7.4. The diffraction experiment

H. J. Bernsteina*

aDepartment of Mathematics and Computer Science, Kramer Science Center, Dowling College, Idle Hour Blvd, Oakdale, NY 11769, USA
Correspondence e-mail: yaya@bernstein-plus-sons.com

3.7.4. The diffraction experiment

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The categories relating to the diffraction experiment are as follows:

DIFFRN group
Frames of data (§3.7.4.1[link])
 DIFFRN_DATA_FRAME
The detector apparatus (§3.7.4.2[link])
 DIFFRN_DETECTOR
 DIFFRN_DETECTOR_AXIS
 DIFFRN_DETECTOR_ELEMENT
Apparatus and instrumentation at the crystal (§3.7.4.3[link])
 DIFFRN_MEASUREMENT
 DIFFRN_MEASUREMENT_AXIS
The radiation source (§3.7.4.4[link])
 DIFFRN_RADIATION
Intensity measurements (§3.7.4.5[link])
 DIFFRN_REFLN
Diffraction scans (§3.7.4.6[link])
 DIFFRN_SCAN
 DIFFRN_SCAN_AXIS
 DIFFRN_SCAN_FRAME
 DIFFRN_SCAN_FRAME_AXIS

The CBF/imgCIF dictionary extends the mmCIF categories in the DIFFRN group, which are very similar to their corresponding categories in the core CIF dictionary. The DIFFRN group is introduced in the description of the core CIF dictionary in Section 3.2.2.2[link] . Its use in the mmCIF dictionary is described in Section 3.6.5.2[link] , from which we quote: `The categories in the DIFFRN category group describe the diffraction experiment. Data items in the DIFFRN category itself can be used to give overall information about the experiment, such as the temperature and pressure. Examples of the other categories are DIFFRN_DETECTOR, which is used for describing the detector used for data collection, and DIFFRN_SOURCE, which is used to give details of the source of the radiation used in the experiment. Data items in the DIFFRN_REFLN category can be used to give information about the raw data and data items in the DIFFRN_REFLNS category can be used to give information about all the reflection data collectively.' In this chapter we focus on the CBF/imgCIF extensions.

3.7.4.1. Frames of data

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Data items in this category are as follows:

DIFFRN_DATA_FRAME [Scheme scheme8]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

Data items in the DIFFRN_DATA_FRAME category record details about each frame of data. An experiment may produce multiple frames of data and each frame may be constructed from data provided by multiple detector elements. Each complete frame of data is uniquely identified by the value of _diffrn_data_frame.id. The detector elements used are specified by values of _diffrn_data_frame.detector_element_id, which forms the category key together with _diffrn_data_frame.id. _diffrn_data_frame.detector_element_id is a pointer to _diffrn_detector_element.id in the DIFFRN_DETECTOR_ELEMENT category. The structure of the data in the frame is completed by giving values for _diffrn_data_frame.array_id (a pointer to _array_structure.id). The particular blocks of data in the frame are specified by giving values of _diffrn_data_frame.binary_id (a pointer to _array_data.binary_id).

3.7.4.2. The detector apparatus

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Data items in these categories are as follows:

(a) DIFFRN_DETECTOR [Scheme scheme9]

(b) DIFFRN_DETECTOR_AXIS [Scheme scheme10]

(c) DIFFRN_DETECTOR_ELEMENT [Scheme scheme11]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics are defined in the mmCIF dictionary.

The DIFFRN_DETECTOR category is defined in the mmCIF dictionary (Section 3.6.5.2[link] ; see the detailed discussion in Section 3.2.2.2.4[link] ). The CBF/imgCIF dictionary restates the DIFFRN_DETECTOR category, adding new tags. Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. In order to allow for multiple detectors, the category key has been extended to include _diffrn_detector.id to uniquely identify each detector. If there is only one detector, _diffrn_detector.id need not be specified, and it will implicitly default to the value of _diffrn_detector.diffrn_id (a pointer to _diffrn.id in the DIFFRN category in the mmCIF dictionary). The general class of detector is given by the value of _diffrn_detector.detector with the make and model given by the value of _diffrn_detector.type. Any special aspects of the detector not covered elsewhere are given by the value of _diffrn_detector.details. As in mmCIF, the value of _diffrn_detector.dtime gives the deadtime of the detector. Additional data items may need to be added in the future for complex inhomogeneous deadtime situations. In addition, the number of axes can be specified using _diffrn_detector.number_of_axes.

Data items in the DIFFRN_DETECTOR_AXIS category associate axes with detectors. Each axis is associated with a detector through the value of _diffrn_detector_axis.detector_id (a pointer to _diffrn_detector.id). The value of *.axis_id (a pointer to _axis.id) identifies an axis. Together *.detector_id and *.axis_id form the category key.

Data items in the DIFFRN_DETECTOR_ELEMENT category record details about the spatial layout and other characteristics of each element of a detector which may have multiple elements, giving the X and Y coordinates of the position of the beam centre relative to the lower left corner of each detector element. Each detector element is identified by the value of _diffrn_detector_element.id and the detector of which it is an element is identified by the value of _diffrn_detector_element.detector_id (a pointer to _diffrn_detector.id).

In most cases, it would be preferable to use the more detailed information provided in the ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS categories rather than simply specifying the coordinates of the centre of the beam relative to the lower left corner of each detector element.

3.7.4.3. Apparatus and instrumentation at the crystal

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Data items in these categories are as follows:

(a) DIFFRN_MEASUREMENT [Scheme scheme12]

(b) DIFFRN_MEASUREMENT_AXIS [Scheme scheme13]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics are defined in the mmCIF dictionary.

The DIFFRN_MEASUREMENT category is defined in the mmCIF dictionary (Section 3.6.5.2[link] ; see the detailed discussion in Section 3.2.2.2.3[link] ). The CBF/imgCIF dictionary restates the DIFFRN_MEASUREMENT category, adding new tags. Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. To allow for multiple measurement devices, _diffrn_measurement.id has been added to the category key. The number of axes is given by the value of _diffrn_measurement.number_of_axes. The axes should be described using entries in DIFFRN_MEASUREMENT_AXIS.

Data items in the DIFFRN_MEASUREMENT_AXIS category associate axes with goniometers, just as data items in the DIFFRN_DETECTOR_AXIS category associate axes with detectors.

3.7.4.4. The radiation source

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Data items in this category are as follows:

DIFFRN_RADIATION [Scheme scheme14]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics are defined in the mmCIF dictionary.

The DIFFRN_RADIATION category is defined in the mmCIF dictionary (Section 3.6.5.2[link] ; see the detailed discussion in Section 3.2.2.2.2[link] ). The CBF/imgCIF dictionary adds the items _diffrn_radiation.div_x_source, *.div_y_source and *.div_x_y_source to specify beam crossfire, and the items _diffrn_radiation.polarizn_source_norm and *.polarizn_source_ratio to provide a definition of polarization relative to the laboratory coordinate system rather than relative to the diffraction plane. The value of the beam crossfire component _diffrn_radiation.div_x_source is the mean deviation in degrees of the X-ray beam from being parallel to the X axis as it illuminates the sample. The value of the beam crossfire component _diffrn_radiation.div_y_source is the mean deviation in degrees of the X-ray beam from being parallel to the Y axis as it illuminates the sample. The value of the beam crossfire component _diffrn_radiation.div_x_y_source is the correlation of the X and Y components. The value of the normal component of the polarization _diffrn_radiation.polarizn_source_norm is the angle in degrees, as viewed from the specimen, between the normal to the polarization plane and the laboratory Y axis as defined in the AXIS category. The dimensionless value of _diffrn_radiation.polarisn_ratio is the ratio [( I_p - I_n ) /( I_p + I_n )], where [I_n] is the intensity (amplitude squared) of the electric vector of the illumination of the sample normal to the polarization and [I_p] is the intensity of the electric vector of the illumination of the sample in the plane of polarization. With suitable choices of laboratory axes, the definitions conform to synchrotron conventions. See Chapter 4.6[link] for a detailed description of these items.

3.7.4.5. Intensity measurements

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Data items in this category are as follows:

DIFFRN_REFLN [Scheme scheme15]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics are defined in the mmCIF dictionary.

The DIFFRN_REFLN category is defined in the mmCIF dictionary (Section 3.6.5.2[link] ; see the detailed discussion in Section 3.2.2.2.2[link] ). Data items in the DIFFRN_REFLN category record details of the intensities measured in the diffraction data set identified by _diffrn_refln.diffrn_id. The CBF/imgCIF dictionary extends the key with _diffrn_refln.frame_id (a pointer to _diffrn_data_frame.id), so that multiple data sets may be recorded.

3.7.4.6. Diffraction scans

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Data items in these categories are as follows:

(a) DIFFRN_SCAN [Scheme scheme16]

(b) DIFFRN_SCAN_AXIS [Scheme scheme17]

(c) DIFFRN_SCAN_FRAME [Scheme scheme18]

(d) DIFFRN_SCAN_FRAME_AXIS [Scheme scheme19]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

Data items in the DIFFRN_SCAN category describe the parameters of one or more scans, relating axis positions to frames. Each scan is uniquely identified by the value of _diffrn_scan.id. The data items in this category give overall information for the scan. The detailed frame-by-frame data are given in DIFFRN_SCAN_FRAME and DIFFRN_SCAN_FRAME_AXIS. The values of _diffrn_scan.date_start and *.date_end give the starting and ending time for a scan. The original definition of the yyyy-mm-dd data type, which includes date and time, has been extended in the CBF/imgCIF dictionary. This allows the seconds part of the time to include an optional decimal fraction. The approximate average integration time for each step of the scan is given by the value of _diffrn_scan.integration_time. The scan is tied to individual frame IDs by the values of _diffrn_scan.frame_id_start and *.frame_id_end. The number of frames in the scan is given by the value of _diffrn_scan.frames.

Data items in the DIFFRN_SCAN_AXIS category describe the settings of axes for particular scans. Unspecified axes are assumed to be at their zero points. The vector of each axis is not given here, because it is provided in the AXIS category. By making _diffrn_scan_axis.scan_id and _diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category, an arbitrary number of scanning and fixed axes can be specified for a scan. The value of _diffrn_scan_axis.scan_id (a pointer to _diffrn_scan.id) identifies the scan and the values of _diffrn_scan_axis.axis_id (a pointer to _axis.id) associate particular axes with that scan. The steps of each axis are specified by *_start, *_range, *_increment and *_rstrt_incr values for angles or for displacements. The *_start value is the setting of the relevant axis at the start of the scan. The *_range value is the total change in the axis setting through the scan. The *_increment value is the increment in the axis setting for each step of the scan. The *_rstrt_incr value is the increment in the axis setting after each step of the scan.

Data items in the DIFFRN_SCAN_FRAME category describe the relationship of particular frames to scans. The value of _diffrn_scan_frame.frame_id (a pointer to _diffrn_data_frame.id) identifies the frame. The value of _diffrn_scan_frame.scan_id (a pointer to _diffrn_scan.id) identifies the scan of which the frame is a part. Together _diffrn_scan_frame.frame_id and *.scan_id form the category key. The value of _diffrn_scan_frame.date gives the date and time of the start of the data collection for the frame. The value of _diffrn_scan_frame.frame_number gives the number of the frame (starting with 1). The value of _diffrn_scan_frame.integration_time gives the precise time in seconds to integrate this step of the scan.

Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the settings of axes for particular frames. Unspecified axes are assumed to be at their zero points. If for any given frame non-zero values apply for any of the data items in this category, those values should be given explicitly in this category and not simply inferred from values in DIFFRN_SCAN_AXIS. Since the collection for a given frame may involve multiple axes, the frame involved is identified by the value of _diffrn_scan_frame_axis.frame_id (a pointer to _diffrn_data_frame.id) and each axis is identified by the value of _diffrn_scan_frame_axis.axis_id (a pointer to _axis.id). Together _diffrn_scan_frame_axis.frame_id and *.axis_id form the category key. If the axis is an axis of rotation, the axis settings for the frame are given by the values of _diffrn_scan_frame_axis.angle, *.angle_increment and *.angle_rstrt_incr. If the axis is a translation axis, the axis settings for the frame are given by the values of _diffrn_scan_frame_axis.displacement, *.displacement_increment and *.displacement_rstrt_incr. The integration begins at the setting given by the value of _diffrn_scan_frame_axis.angle or of *.displacement. The *_increment value gives the change of axis setting during the scan. At the end of the integration, the axis may need to be repositioned by an additional amount. That amount is given by *_rstrt_incr[link].








































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