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284 bytes added ,  16:14, 29 June 2020
Line 22: Line 22:  
  egrep -v 'JOB|REIDX' XDS.INP > XDS.INP.new
 
  egrep -v 'JOB|REIDX' XDS.INP > XDS.INP.new
 
  echo "! JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT" > XDS.INP
 
  echo "! JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT" > XDS.INP
  echo "JOB=INTEGRATE CORRECT" >> XDS.INP
+
  echo "JOB=DEFPIX INTEGRATE CORRECT" >> XDS.INP
 
  echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 >> XDS.INP ! default is 9
 
  echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 >> XDS.INP ! default is 9
 
  echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13      >> XDS.INP ! default is 9
 
  echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13      >> XDS.INP ! default is 9
Line 28: Line 28:  
  xds_par
 
  xds_par
 
and thereby re-run the INTEGRATE and CORRECT steps. This has the advantage that the refined geometry parameters (from CORRECT) are recycled into INTEGRATE, which sometimes leads to better R-factors. It also results in the spacegroup's restraints on the unit cell parameters being used for the prediction of spot positions; these are therefore slightly more accurate. Fine-slicing of profiles has been found to be advantageous at least for Pilatus detectors ([http://dx.doi.org/10.1107/S0907444911049833 Müller, Wang and Schulze-Briese (2012), Acta Cryst D68, 42]), but this should not be specific for Pilatus.
 
and thereby re-run the INTEGRATE and CORRECT steps. This has the advantage that the refined geometry parameters (from CORRECT) are recycled into INTEGRATE, which sometimes leads to better R-factors. It also results in the spacegroup's restraints on the unit cell parameters being used for the prediction of spot positions; these are therefore slightly more accurate. Fine-slicing of profiles has been found to be advantageous at least for Pilatus detectors ([http://dx.doi.org/10.1107/S0907444911049833 Müller, Wang and Schulze-Briese (2012), Acta Cryst D68, 42]), but this should not be specific for Pilatus.
 +
 +
You may also want to change the INCLUDE_RESOLUTION_RANGE= line in XDS.INP, in particular to adapt the upper resolution parameter. A very good rule is to set this to the resolution value of the highest shell that still has a "*" appended to the CC1/2 value in [[CORRECT.LP]] .
    
=== using the refined values for beam divergence and mosaicity for re-integration ===
 
=== using the refined values for beam divergence and mosaicity for re-integration ===
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