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The IDXREF step of XDS

  1. reads a list of spot positions from SPOT.XDS and converts them to vectors in reciprocal space (which requires suitable values for ORGX, ORGY, DETECTOR_DISTANCE, OSCILLATION_RANGE, X-RAY_WAVELENGTH, QX, QY, DIRECTION_OF_DETECTOR_X-AXIS, DIRECTION_OF_DETECTOR_Y-AXIS, INCIDENT_BEAM_DIRECTION, ROTATION_AXIS, SEPMIN; CLUSTER_RADIUS) - see also XDS.INP#Keywords_which_affect_whether_indexing_will_succeed
  2. calculates primitive unit cell parameters from the (clustered) difference vectors
  3. as a control, prints out indices (which should be close to integer numbers) corresponding to difference vectors
  4. uses the cell thus obtained to evaluate possible alternative origins of reciprocal space close to the one that is calculated from ORGX ORGY
  5. evaluates all possible Bravais lattices corresponding to the primitive unit cell (and gives the unit cell parameters and reindexing transformation for that lattice)
  6. based on the values of UNIT_CELL_PARAMETERS, SPACE_GROUP_NUMBER and REFINE(IDXREF) refines the geometry describing the diffraction experiment and writes the result to XPARM.XDS

As an alternative to UNIT_CELL_PARAMETERS, one may specify UNIT_CELL_A-AXIS, UNIT_CELL_B-AXIS, UNIT_CELL_C-AXIS (with parameters from a previous XDS job). This serves to to maintain a consistent indexing scheme between several data sets taken from the same crystal in the same orientation.

See also

Space group determination