@@ Line 1: / Line 1: @@
+== [[Space group determination]] ==
+The approach to [[space group determination]] is well explained in CORRECT.LP :
+ XDS adopts the following approach.
+ (1) it looks for possible symmetries of the crystal lattice
+ (2) it computes a redundancy independent R-factor for all enantiomorphous
+     point groups compatible with the observed lattice symmetry.
+ (3) it selects the group which explains the intensity data at an acceptable,
+     redundancy-independent R-factor (Rmeas, Rrim) using a minimum number of
+     unique reflections.
+ This approach does not test for the presence of screw axes. Consequently,
+ orthorhombic cell axes will be specified in increasing length (following
+ conventions), despite the possibility that different assignments for the
+ cell axes could become necessary for space groups P222(1) and P2(1)2(1)2
+ containing one or two screw axes, respectively.
+ The user can always override the automatic decisions by specifying the
+ correct space group number and unit cell constants in XDS.INP and repeating
+ the CORRECT step of XDS. This provides a simple way to rename orthorhombic
+ cell constants if screw axes are present.
+ In addition, the user has the option to specify in XDS.INP
+ (a) a reference data set or
+ (b) a reindexing transformation or
+ (c) the three basis vectors (if known from processing a previous data set
+ taken at the same crystal orientation in a multi-wavelength experiment).
+ These features of XDS are useful for resolving the issue of alternative
+ settings of polar or rhombohedral cells (like P4, P6, R3).
+Please note the sentence: '''This approach does not test for the presence of screw axes.''' The information about those reflections that may indicate screw axes is actually given in the table '''"REFLECTIONS OF TYPE H,0,0  0,K,0  0,0,L OR EXPECTED TO BE ABSENT (*)"''' (near the end of CORRECT.LP) but there is no automatic evaluation of that table that would result in screw axis assignment.
+Therefore, the '''space group determination of XDS only results in evaluation of the possible point groups that are compatible with the lattice symmetry'''. [[Space group determination]] of XDS only suggests one representative for each point group - the other possible space groups belonging to its point group are possibilities as well, but are not listed! For example, if XDS suggest space group 89 (P422), then any other space group of point group PG422, like 90, 91, 92, 93, 94, 95 and 96 is equally possible.
+If the user wants more automatic determination, it is suggested to run
+ echo SETTING SYMMETRY-BASED | pointless XDS_ASCII.HKL
+Please note that SETTING SYMMETRY-BASED overrides a [[pointless]] default that would lead to ambiguity between space group numbers and space group symbols for space group numbers 5, 17 and 18. The mapping of numbers and names is:
+ ****** 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]
+== Cell parameter refinement ==
+This may look like
+<pre>
+ ******************************************************************************
+  REFINEMENT OF DIFFRACTION PARAMETERS USING ALL IMAGES
+ ******************************************************************************
+ REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM    197690 INDEXED SPOTS
+ REFINED PARAMETERS:   POSITION BEAM AXIS ORIENTATION CELL
+ STANDARD DEVIATION OF SPOT    POSITION (PIXELS)     0.50
+ STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    0.03
+ SPACE GROUP NUMBER    199
+ UNIT CELL PARAMETERS     77.443    77.443    77.443  90.000  90.000  90.000
+ E.S.D. OF CELL PARAMETERS  1.8E-02 1.8E-02 1.8E-02 0.0E+00 0.0E+00 0.0E+00
+ REC. CELL PARAMETERS   0.012913  0.012913  0.012913  90.000  90.000  90.000
+ COORDINATES OF UNIT CELL A-AXIS    45.490    47.263   -41.162
+ COORDINATES OF UNIT CELL B-AXIS   -45.887    59.759    17.904
+ COORDINATES OF UNIT CELL C-AXIS    42.690    13.873    63.107
+ CRYSTAL MOSAICITY (DEGREES)     0.048
+ LAB COORDINATES OF ROTATION AXIS  0.999999  0.001525 -0.000039
+ DIRECT BEAM COORDINATES (REC. ANGSTROEM)  -0.003439  0.001125  0.999994
+ DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM    2299.53   2261.76
+ DETECTOR ORIGIN (PIXELS) AT                     2308.69   2258.76
+ CRYSTAL TO DETECTOR DISTANCE (mm)       199.65
+ LAB COORDINATES OF DETECTOR X-AXIS  1.000000  0.000000  0.000000
+ LAB COORDINATES OF DETECTOR Y-AXIS  0.000000  1.000000  0.000000
+ THE DATA COLLECTION STATISTICS REPORTED BELOW ASSUMES:
+ SPACE_GROUP_NUMBER=  199
+ UNIT_CELL_CONSTANTS=    77.44    77.44    77.44  90.000  90.000  90.000
+</pre>
+== Scaling information ==
+<pre>
+ ******************************************************************************
+           CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & RESOLUTION
+ ******************************************************************************
+ RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO
+ OUTPUT FILE: XDS_ASCII.HKL
+ THE CALCULATIONS ASSUME         FRIEDEL'S_LAW= TRUE
+ TOTAL NUMBER OF CORRECTION FACTORS DEFINED       40
+ DEGREES OF FREEDOM OF CHI^2 FIT              2649.6
+ CHI^2-VALUE OF FIT OF CORRECTION FACTORS      1.557
+ NUMBER OF CYCLES CARRIED OUT                      3
+ CORRECTION FACTORS for visual inspection by XDS-Viewer DECAY.cbf
+ XMIN=     0.2 XMAX=    99.7 NXBIN=    2
+ YMIN= 0.00100 YMAX= 0.50246 NYBIN=   20
+ NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS       4832
+ ******************************************************************************
+  CORRECTION FACTORS AS FUNCTION OF X (fast) & Y(slow) IN THE DETECTOR PLANE
+ ******************************************************************************
+ RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO
+ OUTPUT FILE: XDS_ASCII.HKL
+ THE CALCULATIONS ASSUME         FRIEDEL'S_LAW= TRUE
+ TOTAL NUMBER OF CORRECTION FACTORS DEFINED       90
+ DEGREES OF FREEDOM OF CHI^2 FIT              2640.3
+ CHI^2-VALUE OF FIT OF CORRECTION FACTORS      1.456
+ NUMBER OF CYCLES CARRIED OUT                      4
+ CORRECTION FACTORS for visual inspection by XDS-Viewer MODPIX.cbf
+ XMIN=   232.6 XMAX=  3623.4 NXBIN=    9
+ YMIN=   313.3 YMAX=  4064.2 NYBIN=   10
+ NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS       4832
+ ******************************************************************************
+   CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & DETECTOR SURFACE POSITION
+ ******************************************************************************
+ RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO
+ OUTPUT FILE: XDS_ASCII.HKL
+ THE CALCULATIONS ASSUME         FRIEDEL'S_LAW= TRUE
+ TOTAL NUMBER OF CORRECTION FACTORS DEFINED       26
+ DEGREES OF FREEDOM OF CHI^2 FIT              2652.0
+ CHI^2-VALUE OF FIT OF CORRECTION FACTORS      1.418
+ NUMBER OF CYCLES CARRIED OUT                      3
+ CORRECTION FACTORS for visual inspection by XDS-Viewer ABSORP.cbf
+ XMIN=     0.2 XMAX=    99.7 NXBIN=    2
+ DETECTOR_SURFACE_POSITION=    1928    2189
+ DETECTOR_SURFACE_POSITION=    2504    2826
+ DETECTOR_SURFACE_POSITION=    1352    2826
+ DETECTOR_SURFACE_POSITION=    1352    1552
+ DETECTOR_SURFACE_POSITION=    2504    1552
+ DETECTOR_SURFACE_POSITION=    3231    2786
+ DETECTOR_SURFACE_POSITION=    2468    3630
+ DETECTOR_SURFACE_POSITION=    1388    3630
+ DETECTOR_SURFACE_POSITION=     625    2786
+ DETECTOR_SURFACE_POSITION=     625    1592
+ DETECTOR_SURFACE_POSITION=    1388     747
+ DETECTOR_SURFACE_POSITION=    2468     747
+ DETECTOR_SURFACE_POSITION=    3231    1592
+ NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS       4832
+</pre>
+=== Details about the error model ===
+<pre>
+******************************************************************************
+    CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES
+ ******************************************************************************
+ The variance v0(I) of the intensity I obtained from counting statistics is
+ replaced by v(I)=a*(v0(I)+b*I^2). The model parameters a, b are chosen to
+ minimize the discrepancies between v(I) and the variance estimated from
+ sample statistics of symmetry related reflections. This model implicates
+ an asymptotic limit ISa=1/SQRT(a*b) for the highest I/Sigma(I) that the
+ experimental setup can produce (Diederichs (2010) Acta Cryst D66, 733-740).
+     a        b          ISa
+.042E+00  2.177E-04   66.41
+</pre>
 == Statistics of reflections ==
@@ Line 12: / Line 200: @@
 == Statistics of observations ==
-XDS, like SCALA and d*TREK, gives statistics about unaveraged and averaged quantities, but in different tables.
+XDS, like e.g. SCALA/aimless and d*TREK, gives statistics about unaveraged (individual observations) and averaged ("merged") quantities, but in different tables.
 The unaveraged values are in a table that is fine-grained in terms of resolution, at the beginning of CORRECT.LP. The Sigma values in that table are corrected to match the RMS scatter.
@@ Line 20: / Line 208: @@
 at first the definitions of the quantities in the table are given, and then the table itself is printed.
-Specifically, the heading of the table which talks about the unaveraged data looks like this:
+Specifically, the heading of the table which talks about the unaveraged data ("observations") looks like this:
    I/Sigma  = mean intensity/Sigma of a reflection in shell
@@ Line 52: / Line 240: @@
 == Statistics of unique reflections ==
-Later tables talk about the averaged intensities:
+Later tables talk about the averaged ("merged") intensities. Please note that I/SIGMA means "average of I/SIGMA", not "average of I" / "average of SIGMA".
@@ Line 109: / Line 297: @@
   NUMBER OF UNIQUE ACCEPTED REFLECTIONS               173398
-Why is there a discrepancy between "total 515976 173389" ''versus'' "NUMBER OF ACCEPTED OBSERVATIONS 516002", and "NUMBER OF UNIQUE ACCEPTED REFLECTIONS 173398" ?? The reason is that the higher numbers ''include'' even those reflections with I < -3*sigma(I), whereas the numbers in the table refer only to those reflections which should be used downstream (for phasing and refinement). Indeed, XDSCONV filters out observations with I<-3*sigma(I).
+Why is there a discrepancy between "total 515976 173389" ''versus'' "NUMBER OF ACCEPTED OBSERVATIONS 516002", and "NUMBER OF UNIQUE ACCEPTED REFLECTIONS 173398" ?? The reason is that the (higher) numbers ''below'' the table ''include'' observations (and unique reflections) with I < -3*sigma(I), whereas the numbers ''in'' the table refer only to those reflections which should be used downstream (for phasing and refinement). Indeed, XDSCONV filters out those unique reflections which have I<-3*sigma(I).
-It should be noted that the alien rejection controlled by [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REJECT_ALIEN= REJECT_ALIEN=] (default 20) will be performed after making this table. So the number of reflections which you will get from XDSCONV is not the same as reported here. If you want to see the statistics of reflections which will be converted by XDSCONV (thus will be used for further process), you should prepare REMOVE.HKL to explicitly specify the reflections which will be thrown away and run CORRECT step again.
+It should also be noted that the alien rejection controlled by [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REJECT_ALIEN= REJECT_ALIEN=] (default 20) will be performed ''after'' making this table. So the number of reflections which you will get from [[XDSCONV]] is not the same as reported here. If you want to see the statistics of reflections which will be converted by XDSCONV (thus will be used for further process), you should prepare REMOVE.HKL to explicitly specify the reflections which will be thrown away and run CORRECT step again.
 At the bottom of CORRECT.LP we find:

CORRECT.LP: Difference between revisions

CORRECT.LP (view source)

Revision as of 22:55, 12 October 2018