DRAFT DICTIONARY CBF/imgCIF Extensions Dictionary | Draft version 1.5 for comment

#

Index

##### Image dictionary (imgCIF) version 1.5.4

# Category DIFFRN_SCAN

Name:
`'diffrn_scan'`

Description:

        Data items in the DIFFRN_SCAN category describe the parameters of one
         or more scans, relating axis positions to frames.

Examples:

Example 1 - derived from a suggestion by R. M. Sweet. 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. In this example, three rotation axes and one translation axis at nonzero values are specified, with one axis stepping. There is no reason why more axes could not have been specified to step. Range information has been specified, but note that it can be calculated from the number of frames and the increment, so the data item _diffrn_scan_axis.angle_range could be dropped. Both the sweep data and the data for a single frame are specified. Note that the information on how the axes are stepped is given twice, once in terms of the overall averages in the value of _diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS, and precisely for the given frame in the value for _diffrn_scan_frame.integration_time and the values for DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to scan times and nonlinear stepping is done, these values may differ. Therefore, in interpreting the data for a particular frame it is important to use the frame-specific data.

          _diffrn_scan.id                   1
          _diffrn_scan.date_start         '2001-11-18T03:26:42'
          _diffrn_scan.date_end           '2001-11-18T03:36:45'
          _diffrn_scan.integration_time    3.0
          _diffrn_scan.frame_id_start      mad_L2_000
          _diffrn_scan.frame_id_end        mad_L2_200
          _diffrn_scan.frames              201

           loop_
          _diffrn_scan_axis.scan_id
          _diffrn_scan_axis.axis_id
          _diffrn_scan_axis.angle_start
          _diffrn_scan_axis.angle_range
          _diffrn_scan_axis.angle_increment
          _diffrn_scan_axis.displacement_start
          _diffrn_scan_axis.displacement_range
          _diffrn_scan_axis.displacement_increment

           1 omega 200.0 20.0 0.1 . . .
           1 kappa -40.0  0.0 0.0 . . .
           1 phi   127.5  0.0 0.0 . . .
           1 tranz  . . .   2.3 0.0 0.0

          _diffrn_scan_frame.scan_id                   1
          _diffrn_scan_frame.date               '2001-11-18T03:27:33'
          _diffrn_scan_frame.integration_time    3.0
          _diffrn_scan_frame.frame_id            mad_L2_018
          _diffrn_scan_frame.frame_number        18

          loop_
          _diffrn_scan_frame_axis.frame_id
          _diffrn_scan_frame_axis.axis_id
          _diffrn_scan_frame_axis.angle
          _diffrn_scan_frame_axis.angle_increment
          _diffrn_scan_frame_axis.displacement
          _diffrn_scan_frame_axis.displacement_increment

           mad_L2_018 omega 201.8  0.1 . .
           mad_L2_018 kappa -40.0  0.0 . .
           mad_L2_018 phi   127.5  0.0 . .
           mad_L2_018 tranz  .     .  2.3 0.0

Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis & H. J. Bernstein). A detector is placed 240 mm along the Z axis from the goniometer. This leads to a choice: either the axes of the detector are defined at the origin, and then a Z setting of -240 is entered, or the axes are defined with the necessary Z offset. In this case, the setting is used and the offset is left as zero. This axis is called DETECTOR_Z. The axis for positioning the detector in the Y direction depends on the detector Z axis. This axis is called DETECTOR_Y. The axis for positioning the detector in the X direction depends on the detector Y axis (and therefore on the detector Z axis). This axis is called DETECTOR_X. This detector may be rotated around the Y axis. This rotation axis depends on the three translation axes. It is called DETECTOR_PITCH. A coordinate system is defined on the face of the detector in terms of 2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to index the first array index of the data array and the ELEMENT_Y axis is used to index the second array index. Because the pixels are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075, 0.075) in this coordinate system.

         ###CBF: VERSION 1.1

         data_image_1

         # category DIFFRN
         _diffrn.id P6MB
         _diffrn.crystal_id P6MB_CRYSTAL7

         # category DIFFRN_SOURCE
         loop_
         _diffrn_source.diffrn_id
         _diffrn_source.source
         _diffrn_source.type
          P6MB synchrotron 'SSRL beamline 9-1'

         # category DIFFRN_RADIATION
         loop_
         _diffrn_radiation.diffrn_id
         _diffrn_radiation.wavelength_id
         _diffrn_radiation.monochromator
         _diffrn_radiation.polarizn_source_ratio
         _diffrn_radiation.polarizn_source_norm
         _diffrn_radiation.div_x_source
         _diffrn_radiation.div_y_source
         _diffrn_radiation.div_x_y_source
          P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
         0.01 0.00

         # category DIFFRN_RADIATION_WAVELENGTH
         loop_
         _diffrn_radiation_wavelength.id
         _diffrn_radiation_wavelength.wavelength
         _diffrn_radiation_wavelength.wt
          WAVELENGTH1 0.98 1.0

         # category DIFFRN_DETECTOR
         loop_
         _diffrn_detector.diffrn_id
         _diffrn_detector.id
         _diffrn_detector.type
         _diffrn_detector.number_of_axes
          P6MB MAR345-SN26 'MAR 345' 4

         # category DIFFRN_DETECTOR_AXIS
         loop_
         _diffrn_detector_axis.detector_id
         _diffrn_detector_axis.axis_id
          MAR345-SN26 DETECTOR_X
          MAR345-SN26 DETECTOR_Y
          MAR345-SN26 DETECTOR_Z
          MAR345-SN26 DETECTOR_PITCH

         # category DIFFRN_DETECTOR_ELEMENT
         loop_
         _diffrn_detector_element.id
         _diffrn_detector_element.detector_id
          ELEMENT1 MAR345-SN26

         # category DIFFRN_DATA_FRAME
         loop_
         _diffrn_data_frame.id
         _diffrn_data_frame.detector_element_id
         _diffrn_data_frame.array_id
         _diffrn_data_frame.binary_id
          FRAME1 ELEMENT1 ARRAY1 1

         # category DIFFRN_MEASUREMENT
         loop_
         _diffrn_measurement.diffrn_id
         _diffrn_measurement.id
         _diffrn_measurement.number_of_axes
         _diffrn_measurement.method
          P6MB GONIOMETER 3 rotation

         # category DIFFRN_MEASUREMENT_AXIS
         loop_
         _diffrn_measurement_axis.measurement_id
         _diffrn_measurement_axis.axis_id
          GONIOMETER GONIOMETER_PHI
          GONIOMETER GONIOMETER_KAPPA
          GONIOMETER GONIOMETER_OMEGA

         # category DIFFRN_SCAN
         loop_
         _diffrn_scan.id
         _diffrn_scan.frame_id_start
         _diffrn_scan.frame_id_end
         _diffrn_scan.frames
          SCAN1 FRAME1 FRAME1 1

         # category DIFFRN_SCAN_AXIS
         loop_
         _diffrn_scan_axis.scan_id
         _diffrn_scan_axis.axis_id
         _diffrn_scan_axis.angle_start
         _diffrn_scan_axis.angle_range
         _diffrn_scan_axis.angle_increment
         _diffrn_scan_axis.displacement_start
         _diffrn_scan_axis.displacement_range
         _diffrn_scan_axis.displacement_increment
          SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
          SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
          SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
          SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
          SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
          SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
          SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0

         # category DIFFRN_SCAN_FRAME
         loop_
         _diffrn_scan_frame.frame_id
         _diffrn_scan_frame.frame_number
         _diffrn_scan_frame.integration_time
         _diffrn_scan_frame.scan_id
         _diffrn_scan_frame.date
          FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48

         # category DIFFRN_SCAN_FRAME_AXIS
         loop_
         _diffrn_scan_frame_axis.frame_id
         _diffrn_scan_frame_axis.axis_id
         _diffrn_scan_frame_axis.angle
         _diffrn_scan_frame_axis.displacement
          FRAME1 GONIOMETER_OMEGA 12.0 0.0
          FRAME1 GONIOMETER_KAPPA 23.3 0.0
          FRAME1 GONIOMETER_PHI -165.8 0.0
          FRAME1 DETECTOR_Z 0.0 -240.0
          FRAME1 DETECTOR_Y 0.0 0.6
          FRAME1 DETECTOR_X 0.0 -0.5
          FRAME1 DETECTOR_PITCH 0.0 0.0

         # category AXIS
         loop_
         _axis.id
         _axis.type
         _axis.equipment
         _axis.depends_on
         _axis.vector[1] _axis.vector[2] _axis.vector[3]
         _axis.offset[1] _axis.offset[2] _axis.offset[3]
          GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
          GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
          0 0.76604 . . .
          GONIOMETER_PHI   rotation goniometer GONIOMETER_KAPPA 1 0 0
         . . .
          SOURCE           general source . 0 0 1 . . .
          GRAVITY          general gravity . 0 -1 0 . . .
          DETECTOR_Z       translation detector . 0 0 1 0 0 0
          DETECTOR_Y       translation detector DETECTOR_Z 0 1 0 0 0 0
          DETECTOR_X       translation detector DETECTOR_Y 1 0 0 0 0 0
          DETECTOR_PITCH   rotation    detector DETECTOR_X 0 1 0 0 0 0
          ELEMENT_X        translation detector DETECTOR_PITCH
         1 0 0 172.43 -172.43 0
          ELEMENT_Y        translation detector ELEMENT_X
         0 1 0 0 0 0

         # category ARRAY_STRUCTURE_LIST
         loop_
         _array_structure_list.array_id
         _array_structure_list.index
         _array_structure_list.dimension
         _array_structure_list.precedence
         _array_structure_list.direction
         _array_structure_list.axis_set_id
          ARRAY1 1 2300 1 increasing ELEMENT_X
          ARRAY1 2 2300 2 increasing ELEMENT_Y

         # category ARRAY_STRUCTURE_LIST_AXIS
         loop_
         _array_structure_list_axis.axis_set_id
         _array_structure_list_axis.axis_id
         _array_structure_list_axis.displacement
         _array_structure_list_axis.displacement_increment
          ELEMENT_X ELEMENT_X 0.075 0.150
          ELEMENT_Y ELEMENT_Y 0.075 0.150

         # category ARRAY_ELEMENT_SIZE
         loop_
         _array_element_size.array_id
         _array_element_size.index
         _array_element_size.size
          ARRAY1 1 150e-6
          ARRAY1 2 150e-6

         # category ARRAY_INTENSITIES
         loop_
         _array_intensities.array_id
         _array_intensities.binary_id
         _array_intensities.linearity
         _array_intensities.gain
         _array_intensities.gain_esd
         _array_intensities.overload
         _array_intensities.undefined_value
          ARRAY1 1 linear 1.15 0.2 240000 0

          # category ARRAY_STRUCTURE
          loop_
          _array_structure.id
          _array_structure.encoding_type
          _array_structure.compression_type
          _array_structure.byte_order
          ARRAY1 "signed 32-bit integer" packed little_endian

         # category ARRAY_DATA
         loop_
         _array_data.array_id
         _array_data.binary_id
         _array_data.data
          ARRAY1 1
         ;
         --CIF-BINARY-FORMAT-SECTION--
         Content-Type: application/octet-stream;
             conversions="X-CBF_PACKED"
         Content-Transfer-Encoding: BASE64
         X-Binary-Size: 3801324
         X-Binary-ID: 1
         X-Binary-Element-Type: "signed 32-bit integer"
         Content-MD5: 07lZFvF+aOcW85IN7usl8A==

         AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
         ...
         8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE

         --CIF-BINARY-FORMAT-SECTION----
         ;

Example 3 - Example 2 revised for a spiral scan (R. M. Sweet, P. J. Ellis & H. J. Bernstein). A detector is placed 240 mm along the Z axis from the goniometer, as in Example 2 above, but in this example the image plate is scanned in a spiral pattern from the outside edge in. The axis for positioning the detector in the Y direction depends on the detector Z axis. This axis is called DETECTOR_Y. The axis for positioning the detector in the X direction depends on the detector Y axis (and therefore on the detector Z axis). This axis is called DETECTOR_X. This detector may be rotated around the Y axis. This rotation axis depends on the three translation axes. It is called DETECTOR_PITCH. A coordinate system is defined on the face of the detector in terms of a coupled rotation axis and radial scan axis to form a spiral scan. The rotation axis is called ELEMENT_ROT and the radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch and a 75 micrometre 'constant velocity' angular pitch are assumed. Indexing is carried out first on the rotation axis and the radial axis is made to be dependent on it. The two axes are coupled to form an axis set ELEMENT_SPIRAL.

         ###CBF: VERSION 1.1

         data_image_1

         # category DIFFRN
         _diffrn.id P6MB
         _diffrn.crystal_id P6MB_CRYSTAL7

         # category DIFFRN_SOURCE
         loop_
         _diffrn_source.diffrn_id
         _diffrn_source.source
         _diffrn_source.type
          P6MB synchrotron 'SSRL beamline 9-1'

         # category DIFFRN_RADIATION
              loop_
         _diffrn_radiation.diffrn_id
         _diffrn_radiation.wavelength_id
         _diffrn_radiation.monochromator
         _diffrn_radiation.polarizn_source_ratio
         _diffrn_radiation.polarizn_source_norm
         _diffrn_radiation.div_x_source
         _diffrn_radiation.div_y_source
         _diffrn_radiation.div_x_y_source
          P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
         0.01 0.00

         # category DIFFRN_RADIATION_WAVELENGTH
         loop_
         _diffrn_radiation_wavelength.id
         _diffrn_radiation_wavelength.wavelength
         _diffrn_radiation_wavelength.wt
          WAVELENGTH1 0.98 1.0

         # category DIFFRN_DETECTOR
         loop_
         _diffrn_detector.diffrn_id
         _diffrn_detector.id
         _diffrn_detector.type
         _diffrn_detector.number_of_axes
          P6MB MAR345-SN26 'MAR 345' 4

         # category DIFFRN_DETECTOR_AXIS
         loop_
         _diffrn_detector_axis.detector_id
         _diffrn_detector_axis.axis_id
          MAR345-SN26 DETECTOR_X
          MAR345-SN26 DETECTOR_Y
          MAR345-SN26 DETECTOR_Z
          MAR345-SN26 DETECTOR_PITCH

         # category DIFFRN_DETECTOR_ELEMENT
         loop_
         _diffrn_detector_element.id
         _diffrn_detector_element.detector_id
          ELEMENT1 MAR345-SN26

         # category DIFFRN_DATA_FRAME
         loop_
         _diffrn_data_frame.id
         _diffrn_data_frame.detector_element_id
         _diffrn_data_frame.array_id
         _diffrn_data_frame.binary_id
          FRAME1 ELEMENT1 ARRAY1 1

         # category DIFFRN_MEASUREMENT
         loop_
         _diffrn_measurement.diffrn_id
         _diffrn_measurement.id
         _diffrn_measurement.number_of_axes
         _diffrn_measurement.method
          P6MB GONIOMETER 3 rotation

         # category DIFFRN_MEASUREMENT_AXIS
         loop_
         _diffrn_measurement_axis.measurement_id
         _diffrn_measurement_axis.axis_id
          GONIOMETER GONIOMETER_PHI
          GONIOMETER GONIOMETER_KAPPA
          GONIOMETER GONIOMETER_OMEGA

         # category DIFFRN_SCAN
         loop_
         _diffrn_scan.id
         _diffrn_scan.frame_id_start
         _diffrn_scan.frame_id_end
         _diffrn_scan.frames
          SCAN1 FRAME1 FRAME1 1

         # category DIFFRN_SCAN_AXIS
         loop_
         _diffrn_scan_axis.scan_id
         _diffrn_scan_axis.axis_id
         _diffrn_scan_axis.angle_start
         _diffrn_scan_axis.angle_range
         _diffrn_scan_axis.angle_increment
         _diffrn_scan_axis.displacement_start
         _diffrn_scan_axis.displacement_range
         _diffrn_scan_axis.displacement_increment
          SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
          SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
          SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
          SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
          SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
          SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
          SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0

         # category DIFFRN_SCAN_FRAME
         loop_
         _diffrn_scan_frame.frame_id
         _diffrn_scan_frame.frame_number
         _diffrn_scan_frame.integration_time
         _diffrn_scan_frame.scan_id
         _diffrn_scan_frame.date
          FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48

         # category DIFFRN_SCAN_FRAME_AXIS
         loop_
         _diffrn_scan_frame_axis.frame_id
         _diffrn_scan_frame_axis.axis_id
         _diffrn_scan_frame_axis.angle
         _diffrn_scan_frame_axis.displacement
          FRAME1 GONIOMETER_OMEGA 12.0 0.0
          FRAME1 GONIOMETER_KAPPA 23.3 0.0
          FRAME1 GONIOMETER_PHI -165.8 0.0
          FRAME1 DETECTOR_Z 0.0 -240.0
          FRAME1 DETECTOR_Y 0.0 0.6
          FRAME1 DETECTOR_X 0.0 -0.5
          FRAME1 DETECTOR_PITCH 0.0 0.0

         # category AXIS
         loop_
         _axis.id
         _axis.type
         _axis.equipment
         _axis.depends_on
         _axis.vector[1] _axis.vector[2] _axis.vector[3]
         _axis.offset[1] _axis.offset[2] _axis.offset[3]
          GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
          GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
          0 0.76604 . . .
          GONIOMETER_PHI   rotation goniometer GONIOMETER_KAPPA 1 0 0
         . . .
          SOURCE           general source . 0 0 1 . . .
          GRAVITY          general gravity . 0 -1 0 . . .
          DETECTOR_Z       translation detector . 0 0 1 0 0 0
          DETECTOR_Y       translation detector DETECTOR_Z 0 1 0 0 0 0
          DETECTOR_X       translation detector DETECTOR_Y 1 0 0 0 0 0
          DETECTOR_PITCH   rotation    detector DETECTOR_X 0 1 0 0 0 0
          ELEMENT_ROT      translation detector DETECTOR_PITCH 0 0 1 0 0 0
          ELEMENT_RAD      translation detector ELEMENT_ROT 0 1 0 0 0 0

         # category ARRAY_STRUCTURE_LIST
         loop_
         _array_structure_list.array_id
         _array_structure_list.index
         _array_structure_list.dimension
         _array_structure_list.precedence
         _array_structure_list.direction
         _array_structure_list.axis_set_id
          ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL

         # category ARRAY_STRUCTURE_LIST_AXIS
         loop_
         _array_structure_list_axis.axis_set_id
         _array_structure_list_axis.axis_id
         _array_structure_list_axis.angle
         _array_structure_list_axis.displacement
         _array_structure_list_axis.angular_pitch
         _array_structure_list_axis.radial_pitch
          ELEMENT_SPIRAL ELEMENT_ROT 0    .  0.075   .
          ELEMENT_SPIRAL ELEMENT_RAD . 172.5  .    -0.150

         # category ARRAY_ELEMENT_SIZE
         # the actual pixels are 0.075 by 0.150 mm
         # We give the coarser dimension here.
         loop_
         _array_element_size.array_id
         _array_element_size.index
         _array_element_size.size
          ARRAY1 1 150e-6

         # category ARRAY_INTENSITIES
         loop_
         _array_intensities.array_id
         _array_intensities.binary_id
         _array_intensities.linearity
         _array_intensities.gain
         _array_intensities.gain_esd
         _array_intensities.overload
         _array_intensities.undefined_value
          ARRAY1 1 linear 1.15 0.2 240000 0

          # category ARRAY_STRUCTURE
          loop_
          _array_structure.id
          _array_structure.encoding_type
          _array_structure.compression_type
          _array_structure.byte_order
          ARRAY1 "signed 32-bit integer" packed little_endian

         # category ARRAY_DATA
         loop_
         _array_data.array_id
         _array_data.binary_id
         _array_data.data
          ARRAY1 1
         ;
         --CIF-BINARY-FORMAT-SECTION--
         Content-Type: application/octet-stream;
             conversions="X-CBF_PACKED"
         Content-Transfer-Encoding: BASE64
         X-Binary-Size: 3801324
         X-Binary-ID: 1
         X-Binary-Element-Type: "signed 32-bit integer"
         Content-MD5: 07lZFvF+aOcW85IN7usl8A==

         AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
         ...
         8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE

         --CIF-BINARY-FORMAT-SECTION----
         ;

Category groups:
`inclusive_group`
`diffrn_group`
Category key:
`_diffrn_scan.id`

Mandatory category: no

#### HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:

Copyright © 2005 International Union of Crystallography