IDXREF.LP

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IDXREF.LP is the logfile of the IDXREF "job". It reports on aspects of the analysis of difference vectors, the lattice(s) encountered, their interpretation in terms of 44 Bravais lattices, and the refinement of all geometric parameters of the experiment based on the strong reflections identified in the SPOT_RANGE by COLSPOT.

In the following, extracts from a typical IDXREF.LP are shown, together with comments, in the order as they occur.

Listing of parameter values used for indexing

INPUT PARAMETER VALUES
----------------------
NAME_TEMPLATE_OF_DATA_FRAMES=../kb/G3-16mer-A2-1_1_???.img TIFF
STARTING_ANGLE=        0.0000     STARTING_FRAME=       1
NX=  3072  NY=  3072    QX=  0.073242  QY=  0.073242
ROTATION_AXIS=  1.000000  0.000000  0.000000
OSCILLATION_RANGE=    1.0000
X-RAY_WAVELENGTH=       1.000000
INCIDENT_BEAM_DIRECTION=  0.000000  0.000000  1.000000
DIRECTION_OF_DETECTOR_X-AXIS=   1.00000   0.00000   0.00000
DIRECTION_OF_DETECTOR_Y-AXIS=   0.00000   1.00000   0.00000
DETECTOR_DISTANCE=   349.994
ORGX=   1532.00  ORGY=   1566.00
INDEX_MAGNITUDE=   8    INDEX_ERROR=   0.050    INDEX_QUALITY=  0.80
SEPMIN=  6.00    CLUSTER_RADIUS=     3
MAXIMUM_ERROR_OF_SPOT_POSITION=   3.0
MAXIMUM_ERROR_OF_SPINDLE_POSITION=   2.0
SPACE GROUP AND CELL PARAMETERS ARE UNKNOWN

The values shown are taken from XDS.INP, or if not given there, the defaults are output. "SPACE GROUP AND CELL PARAMETERS ARE UNKNOWN" means that XDS.INP had SPACE_GROUP_NUMBER=0

Which data were used for indexing?

AUTOINDEXING IS BASED ON   4043 SPOTS
LOCATED IN THE TRUSTED_REGION= 0.00 1.20 OF THE DETECTOR
OF THE FOLLOWING DATA IMAGES:
SPOT_RANGE=       1      90

The "SPOTS" mentioned above are read from SPOT.XDS, and are collected by COLSPOT. Nota bene: SPOT.XDS is a text file and could be written by a custom program, or a SPOT.XDS written by COLSPOT could be modified afterwards - see Indexing!


Determination of the reciprocal lattice basis

NUMBER OF DIFFERENCE VECTOR CLUSTERS USED                     198
MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels)   3
MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel)    6.0
MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS   0.1256E-02
OBSERVED BASIS CELL VOLUME                             0.1080E+07
DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS   3
  #  COORDINATES OF REC. BASIS VECTOR    LENGTH   1/LENGTH
   1   0.0040197-0.0034658 0.0044763  0.0069432     144.03
   2   0.0060960 0.0063989-0.0005531  0.0088551     112.93
   3  -0.0064850 0.0072590 0.0114902  0.0150590      66.41

Above, the values of CLUSTER_RADIUS (3) and SEPMIN (6.0) are repeated. The reciprocal cell axis lengths (given as 1/LENGTH) are derived from the difference vectors between reciprocal lattice points. If the user supplies UNIT_CELL_CONSTANTS (and SPACE_GROUP_NUMBER is >0), then the supplied unit cell axes are matched here against the observed difference vectors.

The output continues with showing the difference vectors in h,k,l units - ideally these should be close to integral numbers (1, 2 3, ...), which they are in this example:

CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS 
  #  COORDINATES OF VECTOR CLUSTER   FREQUENCY       CLUSTER INDICES   
   1 -0.0040208 0.0034733-0.0044142      991.     -0.99      0.00      0.00
   2 -0.0101816-0.0029195-0.0037781      945.     -0.99     -1.01      0.01
   3 -0.0122581-0.0127817 0.0012276      937.      0.00     -2.00      0.01
   4 -0.0061055-0.0064076 0.0006063      921.      0.00     -1.00      0.00
   5 -0.0020733-0.0098616 0.0050198      904.      1.00     -1.00      0.00
   6 -0.0080465 0.0069232-0.0089221      848.     -2.00      0.00      0.00
   7 -0.0141979 0.0005603-0.0082059      844.     -1.99     -1.00      0.01
   8  0.0064218-0.0072694-0.0114905      801.      0.00     -0.01     -1.00
   9 -0.0019301 0.0133409-0.0094462      794.     -1.99      1.00      0.00
  10 -0.0206410 0.0078000 0.0032924      757.     -1.98     -1.00      1.01
  11 -0.0203128-0.0058325-0.0075707      744.     -1.98     -2.01      0.02
  12 -0.0023531 0.0037679 0.0159009      740.      1.01      0.01      0.99
...
  58  0.0000713 0.0231797-0.0145601      486.     -3.01      1.99      0.00
  59 -0.0119425-0.0263910-0.0096567      482.      0.00     -3.01     -0.99
  60 -0.0117272-0.0032032-0.0242257      480.     -3.00     -1.00     -0.99
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
    66.41    112.93    144.03     89.86     89.89     89.76
  #  COORDINATES OF REC. BASIS VECTOR    REDUCED CELL INDICES
   1   0.0040197-0.0034658 0.0044763     0.00    0.00    1.00
   2   0.0060960 0.0063989-0.0005531     0.00    1.00    0.00
   3  -0.0064850 0.0072590 0.0114902    -1.00    0.00    0.00

From the difference vectors, the "reduced cell" (essentially a P1 cell, with a<b<c) has been established, together with its axes and angles. Furthermore the relation of the reciprocal cell axes (found in the beginning) with respect to the reduced cell is given. If the user supplies UNIT_CELL_CONSTANTS (and SPACE_GROUP_NUMBER >0 ) then these are converted to a reduced cell and given here.


Results from local indexing

RESULTS FROM LOCAL INDEXING OF   3000 OBSERVED SPOTS *****
MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED    8
MAXIMUM ALLOWED DEVIATION FROM INTEGERAL INDICES     0.050
MIMINUM QUALITY OF INDICES FOR EACH SPOT IN A SUBTREE    0.80
QUALITY OF INDICES REQUIRED TO INCLUDE SECOND SUBTREE    0.00
NUMBER OF SUBTREES    118
SUBTREE    POPULATION
    1         2873
    2            6
    3            3
    4            2
    5            2
    6            2
...

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!