Old way of Space group determination: Difference between revisions

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Space group determination can be done within XDS by following these steps:
Space group determination can be done within [[XDS]] by following these steps:
* an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line)
* an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line)
* after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE" in [[IDXREF.LP]] (see the example below).
* after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table '''DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE''' in [[IDXREF.LP]] (see the example below).
* for each possible lattice character, starting with the one corresponding to highest symmetry, do:
* for each possible lattice character, starting with the one corresponding to highest symmetry, do:
** look up space groups corresponding to lattice characters from the list BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS in [[IDXREF.LP]] (repeated at bottom of this article).
** look up space groups corresponding to lattice characters from the list '''BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS''' in [[IDXREF.LP]] (repeated at bottom of this article).
** modify SPACE_GROUP_NUMBER=<number according to that list>
** modify SPACE_GROUP_NUMBER=<number according to that list>
** modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table>
** modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table>
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* repeat for each possible lattice character and finally decide on space group(s)
* repeat for each possible lattice character and finally decide on space group(s)


Example of table "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE":
Example:
   LATTICE-  BRAVAIS-  QUALITY  UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)  REINDEXING CARD (CORRECT)
   LATTICE-  BRAVAIS-  QUALITY  UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)  REINDEXING CARD (CORRECT)
  CHARACTER  LATTICE    OF FIT      a      b      c  alpha  beta gamma
  CHARACTER  LATTICE    OF FIT      a      b      c  alpha  beta gamma
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     43        mI        999.0    219.4  537.2  164.1 107.7 138.4  66.0  -1  1  0  0 -1  1 -2  0  0 -1  0  0
     43        mI        999.0    219.4  537.2  164.1 107.7 138.4  66.0  -1  1  0  0 -1  1 -2  0  0 -1  0  0
     44        aP          0.0    145.8  164.1  245.4  90.1  90.0  90.1  -1  0  0  0  0  1  0  0  0  0 -1  0
     44        aP          0.0    145.8  164.1  245.4  90.1  90.0  90.1  -1  0  0  0  0  1  0  0  0  0 -1  0
This list is somewhat easier to go through by running [[jiffies|sortlattices]] - the top 12 sorted by "Quality of Fit (QoF)" are:
This list is easier to digest by running [[jiffies|sortlattices]] - the top 12 sorted by "Quality of Fit (QoF)" are:
     44        aP          0.0    145.8  164.1  245.4  90.1  90.0  90.1  -1  0  0  0  0  1  0  0  0  0 -1  0
     44        aP          0.0    145.8  164.1  245.4  90.1  90.0  90.1  -1  0  0  0  0  1  0  0  0  0 -1  0
     31        aP          0.3    145.8  164.1  245.4  89.9  90.0  89.9    1  0  0  0  0  1  0  0  0  0  1  0
     31        aP          0.3    145.8  164.1  245.4  89.9  90.0  89.9    1  0  0  0  0  1  0  0  0  0  1  0
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     37        mC        250.3    511.9  145.8  164.1  90.1  90.1  73.5  -1  0 -2  0 -1  0  0  0  0  1  0  0
     37        mC        250.3    511.9  145.8  164.1  90.1  90.1  73.5  -1  0 -2  0 -1  0  0  0  0  1  0  0
Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive).
Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive).
One would thus look up, in the list at the bottom, the different space groups for oP (of which P212121 is most likely), and then re-run CORRECT with
SPACE_GROUP_NUMBER= 19
UNIT_CELL_PARAMETERS= 145.8  164.1  245.4 90 90 90 ! note that all angles must be exactly 90°
REIDX= -1  0  0  0  0  1  0  0  0  0 -1  0
If the R-factors are good, one should then inspect the table '''REFLECTIONS OF TYPE H,0,0  0,K,0  0,0,L OR EXPECTED TO BE ABSENT (*)''' in [[CORRECT.LP]] to find out if the expected screw axes are indeed there.


  BRAVAIS-            POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
  BRAVAIS-            POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS

Revision as of 13:36, 16 November 2007

Space group determination can be done within XDS by following these steps:

  • an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line)
  • after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE in IDXREF.LP (see the example below).
  • for each possible lattice character, starting with the one corresponding to highest symmetry, do:
    • look up space groups corresponding to lattice characters from the list BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS in IDXREF.LP (repeated at bottom of this article).
    • modify SPACE_GROUP_NUMBER=<number according to that list>
    • modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table>
    • modify or insert UNIT_CELL_PARAMETERS= according to table, but make them obey space group requirements
  • run XDS with JOB=CORRECT. Inspect CORRECT.LP and note R-factors, I/sigma and a and b modifiers of standard deviations
  • repeat for each possible lattice character and finally decide on space group(s)

Example: 

 LATTICE-  BRAVAIS-   QUALITY  UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)  REINDEXING CARD (CORRECT)
CHARACTER  LATTICE     OF FIT      a      b      c   alpha  beta gamma

    1        cF        999.0     329.1  328.9  329.5 120.2  83.7 127.4    1  1 -1  0  1 -1  1  0 -1 -1 -1  0
    2        hR        919.0     219.6  285.4  329.4 114.5  85.4 109.9    1  1  0  0 -1  0 -1  0 -1  1  1  0
    3        cP        919.7     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
    5        cI        999.0     285.4  219.4  294.9  65.5  44.4  70.3   -1  0 -1  0 -1  1  0  0  0  1 -1  0
    4        hR        917.8     219.6  285.4  328.9 114.5  85.5 109.8   -1 -1  0  0  1  0 -1  0  1 -1  1  0
    6        tI        999.0     294.9  285.4  219.4  70.3  65.5  44.4    0  1 -1  0 -1  0 -1  0 -1  1  0  0
    7        tI        999.0     285.4  219.4  294.9  65.5  44.4  70.3   -1  0 -1  0 -1  1  0  0  0  1 -1  0
    8        oI        999.0     219.4  285.4  294.9  44.4  65.5  70.3    1 -1  0  0  1  0  1  0  0 -1  1  0
    9        hR        881.8     145.8  219.4  767.9  91.8 101.0 131.6    1  0  0  0 -1  1  0  0 -1 -1  3  0
   10        mC        135.8     219.4  219.6  245.4  89.9  90.1  96.8    1 -1  0  0  1  1  0  0  0  0  1  0
   11        tP        136.4     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   12        hP        385.3     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   13        oC        135.8     219.4  219.6  245.4  90.1  90.1  83.2   -1  1  0  0  1  1  0  0  0  0 -1  0
   15        tI        632.0     145.8  164.1  537.2  72.3  74.3  90.1   -1  0  0  0  0  1  0  0 -1  1 -2  0
   16        oF        999.0     219.4  219.6  537.2  92.7 114.0  83.2    1 -1  0  0 -1 -1  0  0 -1  1 -2  0
   14        mC        135.2     219.4  219.6  245.4  90.1  90.1  83.2   -1  1  0  0  1  1  0  0  0  0 -1  0
   17        mC        999.0     219.6  219.4  285.4  70.3 109.9  83.2   -1 -1  0  0  1 -1  0  0  1  0  1  0
   18        tI        999.0     294.9  329.4  145.8  63.7  90.0 110.0    0 -1  1  0  1 -1 -1  0  1  0  0  0
   19        oI        999.0     145.8  294.9  329.4  70.0  63.7  90.0   -1  0  0  0  0 -1  1  0 -1  1  1  0
   20        mC        783.5     295.5  294.9  145.8  90.0  90.0 112.4    0  1  1  0  0  1 -1  0 -1  0  0  0
   21        tP        785.1     164.1  245.4  145.8  90.0  90.1  90.1    0  1  0  0  0  0 -1  0 -1  0  0  0
   22        hP        999.0     164.1  245.4  145.8  90.0  90.1  90.1    0  1  0  0  0  0 -1  0 -1  0  0  0
   23        oC        783.2     294.9  295.5  145.8  90.0  90.0  67.6    0  1 -1  0  0 -1 -1  0 -1  0  0  0
   24        hR        999.0     434.5  295.5  145.8  90.0  70.5  87.2   -1  2 -1  0  0 -1 -1  0 -1  0  0  0
   25        mC        782.6     294.9  295.5  145.8  90.0  90.0  67.6    0  1 -1  0  0 -1 -1  0 -1  0  0  0
   26        oF        623.1     145.8  359.0  512.0  83.3 106.6 113.9    1  0  0  0 -1  2  0  0 -1  0  2  0
   27        mC        500.0     359.0  145.8  294.9  90.0 120.5  66.1   -1  2  0  0 -1  0  0  0  0 -1  1  0
   28        mC        252.2     145.8  512.0  164.1  89.9  90.1  73.4   -1  0  0  0 -1  0  2  0  0  1  0  0
   29        mC        251.8     145.8  359.0  245.4  89.9  90.0  66.1    1  0  0  0  1 -2  0  0  0  0 -1  0
   30        mC        315.8     164.1  517.1  145.8  90.0  90.1  71.6    0  1  0  0  0  1 -2  0 -1  0  0  0
   31        aP          0.3     145.8  164.1  245.4  89.9  90.0  89.9    1  0  0  0  0  1  0  0  0  0  1  0
   32        oP          2.8     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   40        oC        315.8     164.1  517.1  145.8  90.0  90.1 108.4    0 -1  0  0  0  1 -2  0  1  0  0  0
   35        mP          0.9     164.1  145.8  245.4  90.0  90.1  90.1    0 -1  0  0  1  0  0  0  0  0  1  0
   36        oC        252.2     145.8  511.9  164.1  89.9  90.1 106.5   -1  0  0  0  1  0  2  0  0  1  0  0
   33        mP          2.5     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   38        oC        251.6     145.8  359.0  245.4  89.9  90.0 113.9    1  0  0  0 -1  2  0  0  0  0  1  0
   34        mP          2.2     145.8  245.4  164.1  90.1  90.1  90.0    1  0  0  0  0  0  1  0  0 -1  0  0
   42        oI        565.2     145.8  164.1  537.2 107.7 105.7  90.1    1  0  0  0  0 -1  0  0 -1  1 -2  0
   41        mC        315.5     517.1  164.1  145.8  90.1  90.0  71.6    0 -1  2  0  0 -1  0  0  1  0  0  0
   37        mC        250.3     511.9  145.8  164.1  90.1  90.1  73.5   -1  0 -2  0 -1  0  0  0  0  1  0  0
   39        mC        249.7     359.0  145.8  245.4  90.0  90.1  66.1    1 -2  0  0  1  0  0  0  0  0  1  0
   43        mI        999.0     219.4  537.2  164.1 107.7 138.4  66.0   -1  1  0  0 -1  1 -2  0  0 -1  0  0
   44        aP          0.0     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0

This list is easier to digest by running sortlattices - the top 12 sorted by "Quality of Fit (QoF)" are: 

   44        aP          0.0     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   31        aP          0.3     145.8  164.1  245.4  89.9  90.0  89.9    1  0  0  0  0  1  0  0  0  0  1  0
   35        mP          0.9     164.1  145.8  245.4  90.0  90.1  90.1    0 -1  0  0  1  0  0  0  0  0  1  0
   34        mP          2.2     145.8  245.4  164.1  90.1  90.1  90.0    1  0  0  0  0  0  1  0  0 -1  0  0
   33        mP          2.5     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   32        oP          2.8     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   14        mC        135.2     219.4  219.6  245.4  90.1  90.1  83.2   -1  1  0  0  1  1  0  0  0  0 -1  0
   10        mC        135.8     219.4  219.6  245.4  89.9  90.1  96.8    1 -1  0  0  1  1  0  0  0  0  1  0
   13        oC        135.8     219.4  219.6  245.4  90.1  90.1  83.2   -1  1  0  0  1  1  0  0  0  0 -1  0
   11        tP        136.4     145.8  164.1  245.4  90.1  90.0  90.1   -1  0  0  0  0  1  0  0  0  0 -1  0
   39        mC        249.7     359.0  145.8  245.4  90.0  90.1  66.1    1 -2  0  0  1  0  0  0  0  0  1  0
   37        mC        250.3     511.9  145.8  164.1  90.1  90.1  73.5   -1  0 -2  0 -1  0  0  0  0  1  0  0

Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive).

One would thus look up, in the list at the bottom, the different space groups for oP (of which P212121 is most likely), and then re-run CORRECT with 

SPACE_GROUP_NUMBER= 19
UNIT_CELL_PARAMETERS= 145.8  164.1  245.4 90 90 90 ! note that all angles must be exactly 90°
REIDX= -1  0  0  0  0  1  0  0  0  0 -1  0

If the R-factors are good, one should then inspect the table REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*) in CORRECT.LP to find out if the expected screw axes are indeed there. 

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]
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