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12,055 bytes added ,  18:20, 9 September 2016
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  OBSERVED BASIS CELL VOLUME                            0.1080E+07
 
  OBSERVED BASIS CELL VOLUME                            0.1080E+07
 
  DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS  3
 
  DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS  3
 
+
 
   #  COORDINATES OF REC. BASIS VECTOR    LENGTH  1/LENGTH
 
   #  COORDINATES OF REC. BASIS VECTOR    LENGTH  1/LENGTH
 
+
 
     1  0.0040197-0.0034658 0.0044763  0.0069432    144.03
 
     1  0.0040197-0.0034658 0.0044763  0.0069432    144.03
 
     2  0.0060960 0.0063989-0.0005531  0.0088551    112.93
 
     2  0.0060960 0.0063989-0.0005531  0.0088551    112.93
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  CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS  
 
  CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS  
 
+
 
   #  COORDINATES OF VECTOR CLUSTER  FREQUENCY      CLUSTER INDICES   
 
   #  COORDINATES OF VECTOR CLUSTER  FREQUENCY      CLUSTER INDICES   
 
     1 -0.0040208 0.0034733-0.0044142      991.    -0.99      0.00      0.00
 
     1 -0.0040208 0.0034733-0.0044142      991.    -0.99      0.00      0.00
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   59 -0.0119425-0.0263910-0.0096567      482.      0.00    -3.01    -0.99
 
   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
 
   60 -0.0117272-0.0032032-0.0242257      480.    -3.00    -1.00    -0.99
 
+
 
  PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
 
  PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
 
     66.41    112.93    144.03    89.86    89.89    89.76
 
     66.41    112.93    144.03    89.86    89.89    89.76
 
+
 
   #  COORDINATES OF REC. BASIS VECTOR    REDUCED CELL INDICES
 
   #  COORDINATES OF REC. BASIS VECTOR    REDUCED CELL INDICES
 
+
 
     1  0.0040197-0.0034658 0.0044763    0.00    0.00    1.00
 
     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
 
     2  0.0060960 0.0063989-0.0005531    0.00    1.00    0.00
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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.
 
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 ==
    
  RESULTS FROM LOCAL INDEXING OF  3000 OBSERVED SPOTS *****
 
  RESULTS FROM LOCAL INDEXING OF  3000 OBSERVED SPOTS *****
 
+
 
  MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED    8
 
  MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED    8
 
  MAXIMUM ALLOWED DEVIATION FROM INTEGERAL INDICES    0.050
 
  MAXIMUM ALLOWED DEVIATION FROM INTEGERAL INDICES    0.050
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  QUALITY OF INDICES REQUIRED TO INCLUDE SECOND SUBTREE    0.00
 
  QUALITY OF INDICES REQUIRED TO INCLUDE SECOND SUBTREE    0.00
 
  NUMBER OF SUBTREES    118
 
  NUMBER OF SUBTREES    118
 
+
 
  SUBTREE    POPULATION
 
  SUBTREE    POPULATION
 
+
 
     1        2873
 
     1        2873
 
     2            6
 
     2            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!
 
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 [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_FRACTION_OF_INDEXED_SPOTS= 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.
 +
 +
 +
== See also ==
 +
 +
[[Indexing]]
2,522

edits

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