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2,515 bytes added ,  12:48, 18 December 2014
→‎IDXREF ends with !!! ERROR !!! message: remedy for case of too short axis, and difference vectors being halved
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  JOB= DEFPIX INTEGRATE CORRECT
 
  JOB= DEFPIX INTEGRATE CORRECT
 
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).
 
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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==== Things to watch out for in IDXREF.LP ====
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The first table "CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS" should show close-to-integer difference vectors. The following is an example how it should ''not'' look like:
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  #  COORDINATES OF REC. BASIS VECTOR    LENGTH  1/LENGTH
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    1  -0.0000476-0.0014008-0.0044654  0.0046802    213.67
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    2  -0.0101960-0.0056194 0.0019466  0.0118037      84.72
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    3  -0.0145331 0.0238225-0.0071754  0.0288134      34.71
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CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS
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  #  COORDINATES OF VECTOR CLUSTER  FREQUENCY      CLUSTER INDICES 
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    1  0.0004199-0.0012633-0.0043826    2442.      0.97    -0.04    -0.00
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    2  0.0101757 0.0060701-0.0019630    2175.    -0.03    -1.02      0.01
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    3 -0.0076118 0.0114167-0.0040603    1965.      0.13      0.04      0.50
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    4  0.0100552 0.0071646 0.0025337    1944.    -1.01    -0.99      0.01
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    5  0.0072840-0.0101455 0.0084405    1841.    -1.10    -0.01    -0.49
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    6  0.0000976 0.0027828 0.0089584    1792.    -2.00      0.00    -0.00
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    7  0.0103103 0.0043851-0.0063902    1790.      0.98    -1.02      0.00
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    8  0.0025742 0.0163995-0.0098507    1760.      0.95    -0.99      0.51
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    9  0.0068686-0.0089437 0.0128884    1724.    -2.08      0.03    -0.49
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  10 -0.0174443 0.0123504 0.0161324    1694.    -4.01      0.99      0.52
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  11  0.0272195-0.0050005-0.0136142    1678.      2.99    -1.97    -0.50
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  ...
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PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
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    34.71    84.72    213.67    90.35    90.27    90.06
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This clearly indicates that the third axis above the table (with 1/length=34.71) actually should be twice that size. If this happens, the histogram of indexed spots often has two equally-large subtrees:
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SUBTREE    POPULATION
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    1          976
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    2          972
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    3          10
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    4            7
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    5            6
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Remedy: take the reduced cell below the table, but double the 34.71, and stick it into the line
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UNIT_CELL_CONSTANTS=69.42    84.72    213.67    90.35    90.27    90.06
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To make XDS use that line, specify
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SPACE_GROUP_NUMBER=1
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and leave the space group determination for later.
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Alternatively, try several well-separated SPOT_RANGEs instead of 1. For example, instead of
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SPOT_RANGE=1 900
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try
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SPOT_RANGE=1 100
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SPOT_RANGE=801 900
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In most cases, this makes IDXREF pick up the correct cell.
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I have seen this working well in many cases of too short cell parameters.
    
=== IDXREF prints !!! WARNING !!! message ===
 
=== IDXREF prints !!! WARNING !!! message ===
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