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401 bytes added ,  10:32, 28 August 2010
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This is a collection of problems and their solution.
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This is a collection of problems and their solutions.
    
== XDS crashes ==
 
== XDS crashes ==
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XDS should never crash (it it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer.  
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XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer.  
    
If it crashes for the second reason, there are three things to try:
 
If it crashes for the second reason, there are three things to try:
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make sure to use the 32bit version of XDS instead - you were trying to run the 64bit version on a 32bit operating system.  
 
make sure to use the 32bit version of XDS instead - you were trying to run the 64bit version on a 32bit operating system.  
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== IDXREF ends with message ==
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== Indexing failures ==
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In case of problems, you should definitively inspect FRAME.cbf, using [[XDS-viewer]] or [[adxv]]).
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FRAME.cbf is written by COLSPOT. It shows the last frame of the SPOT_RANGE, together with spot positions that COLSPOT found, marked with white pixels.
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FRAME.cbf is also written by INTEGRATE (this overwrites the FRAME.cbf written by COLSPOT). It shows the last frame of the DATA_RANGE, and you should make sure that the predictions (circles) match the observed reflections.
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=== IDXREF ends with message ===
    
   !!! ERROR !!! SOLUTION IS INACCURATE
 
   !!! ERROR !!! SOLUTION IS INACCURATE
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  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.
 
  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.
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Well, this is printed out for you to actually read, and take action accordingly. In many cases you just change the JOBS - line in XDS.INP to read
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This is printed out for you to actually read, and take action accordingly. In many cases you just change the JOBS - line in XDS.INP to read
 
  JOB= DEFPIX INTEGRATE CORRECT
 
  JOB= DEFPIX INTEGRATE CORRECT
and then continue to run XDS. In other cases you change other keywords in [[XDS.INP]]. But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).
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and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).  
 
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Furthermore, you should definitively check FRAME.cbf after the XDS run (using [[XDS-viewer]] or [[adxv]]), to make sure that the predictions match the observed reflections.
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== IDXREF does not show the expected lattice ==
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=== IDXREF.LP does not show the expected lattice ===
    
By specifying the spacegroup and unitcell, you tell XDS that it should index based on those reflections that match that spacegroup and unitcell. In a sense, you _force_ that spacegroup and cell. This will discard other (spurious?) reflections, and usually leads to a clean list of Bravais lattice possibilities.
 
By specifying the spacegroup and unitcell, you tell XDS that it should index based on those reflections that match that spacegroup and unitcell. In a sense, you _force_ that spacegroup and cell. This will discard other (spurious?) reflections, and usually leads to a clean list of Bravais lattice possibilities.
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== none of the lattices in IDXREF.LP (except aP) has a good QUALITY OF FIT ==
 
== none of the lattices in IDXREF.LP (except aP) has a good QUALITY OF FIT ==
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It is a good idea to use many frames (e.g. the first half of the DATA_RANGE, as it is done in the [[generate_XDS.INP]] script) for SPOT_RANGE in the COLSPOT and IDXREF steps.  
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It is a good idea to use many frames, e.g. the first half of the DATA_RANGE, as does the [[generate_XDS.INP]] script, for the COLSPOT and IDXREF steps.  
    
It is entirely possible to run COLSPOT for the ''full'' DATA_RANGE, and to try sub-ranges in IDXREF - this means COLSPOT has to be run only once, and the JOBS= line has e.g.  
 
It is entirely possible to run COLSPOT for the ''full'' DATA_RANGE, and to try sub-ranges in IDXREF - this means COLSPOT has to be run only once, and the JOBS= line has e.g.  
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because otherwise the spurious reflections in the other sub-ranges will probably disturb the on-the-fly refinement of parameters.
 
because otherwise the spurious reflections in the other sub-ranges will probably disturb the on-the-fly refinement of parameters.
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I've seen datasets where each reflection had a satellite associated with the main reflection, but separate from it. In such a case it helps to use
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I've seen datasets where each reflection had a satellite associated with the main reflection, but separate from it. This is well visible in FRAME.cbf written by COLSPOT. In such a case it helps to use
 
  MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 12 ! re-run COLSPOT after changing the parameter !
 
  MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 12 ! re-run COLSPOT after changing the parameter !
 
thus doubling (w.r.t. the default of 6) the required spotsize that makes a reflection be used for indexing. In the latest case this made it possible to index cleanly on a single frame (which is actually not uncommon).
 
thus doubling (w.r.t. the default of 6) the required spotsize that makes a reflection be used for indexing. In the latest case this made it possible to index cleanly on a single frame (which is actually not uncommon).
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