Data Category diffrn_scan

General

Category name
diffrn_scan
Required in PDB entries
no
Category group membership
diffrn_group
Used in current PDB entries
No

Category Relationship Diagrams

70
View full category relationship diagram including all dictionary data categories

Category Description

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

NeXus Mapping Details

 
   
    _diffrn_scan.id SCANID
    _diffrn_scan.date_end ENDDATETIME
    _diffrn_scan.date_start STARTDATETIME
    _diffrn_scan.integration_time AVGCOUNTTIME
    _diffrn_scan.frame_id_start FRAMESTARTID
    _diffrn_scan.frame_id_end FRAMEENDID
    _diffrn_scan.frames FRAMES
    _diffrn_scan.time_period TIMEPER
    _diffrn_scan.time_rstrt_incr RSTRTTIME
   
    -->
   
        /CBF_diffrn_scan__SCANID:NXentry
          /CBF_scan_id="SCANID"
          /end_time=ENDDATETIME
          /start_time=STARTDATETIME
          /average_count_time=AVGCOUNTTIME
            @units="sec"
          /average_frame_time=TIMEPER
            @units="sec"
          /average_frame_restart_time=RSTRTTIME
            @units="sec"
          /instrument:NXinstrument
            /CBF_diffrn_detector__DETECTORNAME:NXdetector
              /frame_start_number=FRAMESTARTNO
              /frame_end_number=FRAMEENDNO
   
    FRAMESTARTNO is the value of _diffrn_scan_frame.frame_number
    for which the value of _diffrn_scan_frame.frame_id equals FRAMESTARTID
    FRAMEENDNO is the value of _diffrn_scan_frame.frame_number
    for which the value of _diffrn_scan_frame.frame_id equals FRAMEENDID

Category Examples

3

 
      _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
     ###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
     ;
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         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----
     ;
     ###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
     ;
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     X-Binary-Size: 3801324
     X-Binary-ID: 1
     X-Binary-Element-Type: "signed 32-bit integer"
     Content-MD5: 07lZFvF+aOcW85IN7usl8A==

     AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
     ...
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     --CIF-BINARY-FORMAT-SECTION----
     ;