The IDXREF step of XDS
- 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
- calculates primitive unit cell parameters from the (clustered) difference vectors
- as a control, prints out indices (which should be close to integer numbers) corresponding to difference vectors
- uses the cell thus obtained to evaluate possible alternative origins of reciprocal space close to the one that is calculated from ORGX ORGY
- evaluates all possible Bravais lattices corresponding to the primitive unit cell (and gives the unit cell parameters and reindexing transformation for that lattice)
- 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.