# 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.

## Contents

- 1 Listing of parameter values used for indexing
- 2 Which data were used for indexing?
- 3 Determination of the reciprocal lattice basis
- 4 Results from local indexing
- 5 Finding the origin of the reciprocal lattice (=direct beam position, if normal geometry)
- 6 First refinement of geometry parameters
- 7 Second refinement, after rejecting reflections that do not fit well
- 8 Determination of Bravais lattices consistent with the observed spot positions
- 9 See also

## 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.

**If the difference vectors are not (close to) integers, something is wrong** - see Problems.

## 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!

## 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 0,0,0 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 0 1.0 0.5 1531.7 1566.3 -0.0001 0.0001 1.0000 0.06 0.06 0.10 0 0 -1 4.4 30.4 1550.9 1542.1 0.0039 -0.0050 1.0000 0.13 0.11 0.16 0 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 ***** 1103 OUT OF 4043 SPOTS INDEXED. 0 REJECTED REFLECTIONS (REASON: OVERLAP) 2940 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 , since that fraction is less than MINIMUM_FRACTION_OF_INDEXED_SPOTS (default 0.50).

## Determination of Bravais lattices consistent with the observed spot positions

*********** DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE *********** The CHARACTER OF A LATTICE is defined by the metrical parameters of its reduced cell as described in the INTERNATIONAL TABLES FOR CRYSTALLOGRAPHY Volume A, p. 746 (KLUWER ACADEMIC PUBLISHERS, DORDRECHT/BOSTON/LONDON, 1989). Note that more than one lattice character may have the same BRAVAIS LATTICE. A lattice character is marked "*" to indicate a lattice consistent with the observed locations of the diffraction spots. These marked lattices must have low values for the QUALITY OF FIT and their implicated UNIT CELL CONSTANTS should not violate the ideal values by more than MAXIMUM_ALLOWED_CELL_AXIS_RELATIVE_ERROR= 0.03 MAXIMUM_ALLOWED_CELL_ANGLE_ERROR= 3.0 (Degrees) LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) CHARACTER LATTICE OF FIT a b c alpha beta gamma * 31 aP 0.0 60.8 103.4 132.3 90.0 89.9 89.9 * 44 aP 0.4 60.8 103.4 132.3 90.0 90.1 90.1 * 34 mP 2.1 60.8 132.3 103.4 90.0 90.1 90.1 * 33 mP 2.4 60.8 103.4 132.3 90.0 90.1 90.1 * 35 mP 3.1 103.4 60.8 132.3 90.1 90.0 90.1 * 32 oP 3.5 60.8 103.4 132.3 90.0 90.1 90.1 29 mC 248.7 60.8 215.5 132.3 90.0 90.1 73.7 28 mC 249.1 60.8 271.5 103.4 90.0 90.1 77.1 39 mC 250.2 215.5 60.8 132.3 90.1 90.0 73.7 ... ...

The above list is sorted by the "Quality of fit" - good values are below 10. Triclinic (Bravais lattice "aP") is always the best since it has no restrictions and can thus most easily fit the reduced cell. The unit cell constants are not cleaned to obey the restrictions, e.g. orthorhombic does not necessarily have alpha=beta=gamma=90°. (Please note that, when specifying unit cell constants in XDS.INP, all restrictions have to be met.)

For protein crystals the possible space group numbers corresponding to each Bravais-type are given below for your convenience. Note, that reflection integration is based only on orientation and metric of the lattice. It does not require knowledge of the correct space group! Thus, if no such information is provided by the user in XDS.INP, reflections are integrated assuming a triclinic reduced cell lattice; the space group is assigned automatically or by the user in the last step (CORRECT) when integrated intensities are available. ****** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY ****** BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS TYPE [SPACE GROUP NUMBER,SYMBOL] aP [1,P1] mP [3,P2] [4,P2(1)] mC,mI [5,C2] oP [16,P222] [17,P222(1)] [18,P2(1)2(1)2] [19,P2(1)2(1)2(1)] oC [21,C222] [20,C222(1)] oF [22,F222] oI [23,I222] [24,I2(1)2(1)2(1)] tP [75,P4] [76,P4(1)] [77,P4(2)] [78,P4(3)] [89,P422] [90,P42(1)2] [91,P4(1)22] [92,P4(1)2(1)2] [93,P4(2)22] [94,P4(2)2(1)2] [95,P4(3)22] [96,P4(3)2(1)2] tI [79,I4] [80,I4(1)] [97,I422] [98,I4(1)22] hP [143,P3] [144,P3(1)] [145,P3(2)] [149,P312] [150,P321] [151,P3(1)12] [152,P3(1)21] [153,P3(2)12] [154,P3(2)21] [168,P6] [169,P6(1)] [170,P6(5)] [171,P6(2)] [172,P6(4)] [173,P6(3)] [177,P622] [178,P6(1)22] [179,P6(5)22] [180,P6(2)22] [181,P6(4)22] [182,P6(3)22] hR [146,R3] [155,R32] cP [195,P23] [198,P2(1)3] [207,P432] [208,P4(2)32] [212,P4(3)32] [213,P4(1)32] cF [196,F23] [209,F432] [210,F4(1)32] cI [197,I23] [199,I2(1)3] [211,I432] [214,I4(1)32]

This is just the mapping from Bravais lattice to possible spacegroups.

Maximum oscillation range to prevent angular overlap at high resolution limit assuming zero (!) mosaicity. Maximum oscillation range High resolution limit (degrees) (Angstrom) 2.15 4.00 1.61 3.00 1.07 2.00 0.54 1.00

This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap. The maximum oscillation range is less than that given by the table, since the crystal mosaicity has to be subtracted from the table value. Please see Choice of OSCILLATION RANGE.

cpu time used 2.8 sec elapsed wall-clock time 1.7 sec !!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS AUTOMATIC DATA PROCESSING STOPPED. AS THE CRITERIA FOR A GOOD SOLUTION ARE RATHER STRICT, YOU MAY CHOOSE TO CONTINUE DATA PROCESSING AFTER CHANGING THE "JOB="-CARD IN "XDS.INP" TO "JOB= DEFPIX INTEGRATE CORRECT". IF THE BEST SOLUTION IS REALLY NONSENSE YOU SHOULD FIRST HAVE A LOOK AT THE ASCII-FILE "SPOT.XDS". THIS FILE CONTAINS THE INITIAL SPOT LIST SORTED IN DECREASING SPOT INTENSITY. SPOTS NEAR THE END OF THE FILE MAY BE ARTEFACTS AND SHOULD BE ERASED. ALTERNATIVELY YOU MAY TRY DIFFERENT VALUES FOR "INDEX_ORIGIN" AS SUGGESTED IN THE ABOVE LISTING. IF THE CRYSTAL HAS SLIPPED AT THE BEGINNING OF DATA COLLECTION YOU MAY CHOOSE TO SKIP SOME OF THE FIRST FRAMES BY CHANGING THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.

End of IDXREF.LP. In this case XDS would not automatically continue with the DEFPIX step. Rather, the user has to explicitly state that s/he wants to do this, by changing the JOB line in XDS.INP to

JOB= DEFPIX INTEGRATE CORRECT

This is a feature (not a bug) to make the user aware of a possible problem.