IDXREF.LP: Difference between revisions

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   OBSERVED BASIS CELL VOLUME                             0.1080E+07
   DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS   3
     #  COORDINATES OF REC. BASIS VECTOR    LENGTH   1/LENGTH
    0.0040197-0.0034658 0.0044763  0.0069432     144.03
    0.0060960 0.0063989-0.0005531  0.0088551     112.93
@@ Line 57: / Line 57: @@
   CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS
     #  COORDINATES OF VECTOR CLUSTER   FREQUENCY       CLUSTER INDICES
 -0.0040208 0.0034733-0.0044142      991.     -0.99      0.00      0.00
@@ Line 75: / Line 75: @@
 -0.0119425-0.0263910-0.0096567      482.      0.00     -3.01     -0.99
 -0.0117272-0.0032032-0.0242257      480.     -3.00     -1.00     -0.99
   PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
 .41    112.93    144.03     89.86     89.89     89.76
     #  COORDINATES OF REC. BASIS VECTOR    REDUCED CELL INDICES
    0.0040197-0.0034658 0.0044763     0.00    0.00    1.00
    0.0060960 0.0063989-0.0005531     0.00    1.00    0.00
@@ Line 91: / Line 91: @@
   RESULTS FROM LOCAL INDEXING OF   3000 OBSERVED SPOTS *****
   MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED    8
   MAXIMUM ALLOWED DEVIATION FROM INTEGERAL INDICES     0.050
@@ Line 97: / Line 97: @@
   QUALITY OF INDICES REQUIRED TO INCLUDE SECOND SUBTREE    0.00
   NUMBER OF SUBTREES    118
   SUBTREE    POPULATION
          2873
             6
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 The "subtrees" each refer to their own lattice. The list above indicates that 2873 out of the strongest 3000 reflections can be indexed with a single lattice. 6 reflections correspond to the second-best lattice. If the diffraction pattern arises from split crystals, or there are two (or more) non-equivalent lattices because e.g. ORGX ORGY (in XDS.INP) denote a position right in the middle between two reflections, then several lattices are listed here that have a substantial number of reflections. In such a case IDXREF will choose the lattice with most reflections, but the user should be aware that other lattices exist!
+== Finding the origin of the reciprocal lattice (=direct beam position, if normal geometry) ==
+ ***** SELECTION OF THE INDEX ORIGIN OF THE REFLECTIONS *****
+ The origin of the reflection indices determined so far is
+,0,0 by default which is usually correct. In certain critical
+ cases it may happen that this automatic choice is wrong which
+ leads to misindexing of the reflections by a constant offset.
+ You may replace the default by specifying INDEX_ORIGIN= h k l
+ in the input file "XDS.INP" and rerun the IDXREF step.
+ Below you find a list of possible alternatives together with a
+ measure of their likelihood.
+ QUALITY   small values mean a high likelihood for this offset
+ DELTA     distance between given  1532.00  1566.00 and computed
+           direct beam position (pixels) on the detector
+ XD, YD    computed direct beam position (pixels) on detector
+ X,Y,Z     computed coordinates of the direct beam wave vector
+ DH,DK,DL  mean absolute difference between observed and
+           fitted indices
+  INDEX_   QUALITY  DELTA    XD       YD       X       Y       Z       DH      DK      DL
+  ORIGIN
+  0  0      1.0    0.5   1531.7   1566.3 -0.0001  0.0001  1.0000    0.06    0.06    0.10
+  0 -1      4.4   30.4   1550.9   1542.1  0.0039 -0.0050  1.0000    0.13    0.11    0.16
+  0  1      4.4   31.4   1512.4   1590.6 -0.0041  0.0051  1.0000    0.13    0.11    0.15
+ SELECTED:     INDEX_ORIGIN=  0  0  0
+Errors in the values of ORGX, ORGY (as supplied in XDS.INP) are the most common single source of indexing failure. [[XDS]] tries several possible origins (3 in the example above) around the supplied values and gives an estimate of indexing quality ("QUALITY"; 1.0 is best) for each of them. DH,HK,DL should ideally be 0; they correspond to the deviation of H,K,L from being integer. It is advisable to always use INDEX_ORIGIN= 0 0 0 (the default); if the QUALITY and DH,DK,DL indicators say that the supplied ORGX, ORGY are wrong then the latter should be fixed.
+It is important to realize that ORGX and ORGY are the coordinates of the point of the detector which is closest to the crystal; this is not the same as the direct beam coordinates! However, in practice, at synchrotron beamlines the detector is perpendicular to the beam, in which case taking the direct beam position as ORGY ORGY is accurate enough; IDXREF (and INTEGRATE, CORRECT) refines the beam direction (and other geometric parameters) anyway. This is also why there is no need to specify highly accurate values for BEAM_DIRECTION, ROTATION_AXIS, ORGX, ORGY.
+The word "SELECTED:" may be a bit misleading - XDS does not select the INDEX_ORIGIN, it's the user who does this.
+== First refinement of geometry parameters ==
+ ***** REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 *****
+ REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM   2873 INDEXED SPOTS
+ REFINED PARAMETERS:   DISTANCE BEAM AXIS CELL ORIENTATION
+ STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     5.16
+ STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    4.60
+ CRYSTAL MOSAICITY (DEGREES)     0.200
+ DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.002368  0.008316  0.999963
+ DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1531.82   1565.97
+ DETECTOR ORIGIN (PIXELS) AT                     1541.74   1531.14
+ CRYSTAL TO DETECTOR DISTANCE (mm)       306.77
+ LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
+ LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
+ LAB COORDINATES OF ROTATION AXIS  0.999916 -0.012791 -0.002291
+ COORDINATES OF UNIT CELL A-AXIS    24.214   -28.552   -44.997
+ COORDINATES OF UNIT CELL B-AXIS    68.543    70.993    -7.718
+ COORDINATES OF UNIT CELL C-AXIS    74.857   -62.751    80.778
+ REC. CELL PARAMETERS   0.017084  0.010103  0.007889  90.239  89.766  89.803
+ UNIT CELL PARAMETERS     58.534    98.983   126.753  89.760  90.235  90.198
+ SPACE GROUP NUMBER      1
+Based on the parameters known at this point, and all reflections assigned to the strongest lattice, a first refinement is done.
+== Second refinement, after rejecting reflections that do not fit well ==
+ ***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP #   1 *****
+OUT OF    4043 SPOTS INDEXED.
+REJECTED REFLECTIONS (REASON: OVERLAP)
+REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION)
+ EXPECTED ERROR IN SPINDLE  POSITION     0.809 DEGREES
+ EXPECTED ERROR IN DETECTOR POSITION      1.90 PIXELS
+ ***** DIFFRACTION PARAMETERS USED AT START OF INTEGRATION *****
+ REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM   1103 INDEXED SPOTS
+ REFINED PARAMETERS:   DISTANCE BEAM AXIS CELL ORIENTATION
+ STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     1.86
+ STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.79
+ CRYSTAL MOSAICITY (DEGREES)     0.200
+ DIRECT BEAM COORDINATES (REC. ANGSTROEM)   0.002112  0.014343  0.999895
+ DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    1531.92   1565.77
+ DETECTOR ORIGIN (PIXELS) AT                     1522.67   1502.92
+ CRYSTAL TO DETECTOR DISTANCE (mm)       320.89
+ LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
+ LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
+ LAB COORDINATES OF ROTATION AXIS  0.999918 -0.009393 -0.008744
+ COORDINATES OF UNIT CELL A-AXIS    25.289   -29.852   -46.602
+ COORDINATES OF UNIT CELL B-AXIS    71.309    74.418    -8.739
+ COORDINATES OF UNIT CELL C-AXIS    78.373   -65.138    84.444
+ REC. CELL PARAMETERS   0.016435  0.009668  0.007556  90.014  89.938  89.901
+ UNIT CELL PARAMETERS     60.847   103.437   132.348  89.986  90.062  90.099
+ SPACE GROUP NUMBER      1
+Based on the results from the first refinement, all reflections found by COLSPOT are indexed. In this case, a bit more than 1/4 of these are indexed with low error. This leads to the message "!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS" at the bottom of IDXREF.LP .