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A dataset may be processed by XDS in a single run, provided JOB=ALL (or JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT) is chosen.

However, in many cases one chooses to either

  • go to the next step if XDS does not do so automatically. This can happen for the IDXREF step: if the indexing does not give unambiguous results, XDS stops after IDXREF. If the user decides that the data reduction should be continued (because no error actually exists), XDS can then be run with JOB=DEFPIX INTEGRATE CORRECT. This works because IDXREF, even though it prints an error message, generates the file XPARM.XDS which is required for the DEFPIX and INTEGRATE steps.
  • repeat a step to try different parameter values. This may be the case for IDXREF, to try different space group possibilities. It is also the case for DEFPIX, when trying different values for VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= (inspecting BKGPIX.cbf with XDS-Viewer each time). Or it may be the case for CORRECT, during space group determination, or for Optimization#Optimizing_the_anomalous_signal.
  • go back to an earlier step. See Optimization

In all cases it is important to realize that only those steps need to be repeated which produce different outcomes than those done earlier. For example, for space group determination one only needs to run CORRECT several times, and not IDXREF DEFPIX INTEGRATE CORRECT.