IDXREF.LP
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!