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Space group determination can be done within XDS by following these steps: | == Space group determination with ''pointless'' == | ||
* 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 | The latest and currently easiest way of space group determination from a [[XDS]] formatted reflection file is ''via'' the [[pointless]] program: | ||
echo SETTING SYMMETRY-BASED | pointless xdsin XDS_ASCII.HKL | |||
From the latter pointless output, the correct space group should be deduced and CORRECT run with appropriate SPACE_GROUP_NUMBER and UNIT_CELL_PARAMETERS. | |||
== Space group determination within XDS == | |||
the steps below are not needed anymore since version July-2008 so don't read on! | |||
''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). The [[jiffies|sortlattices]] jiffy is useful here.'' | |||
*'' 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 (e.g. orthorhombic: all angles 90°, tetragonal and trigonal: a=b, and so on).'' | |||
** ''run XDS with JOB=CORRECT. Inspect [[CORRECT.LP]] and note R-factors, I/sigma and a and b modifiers of standard deviations'' | |||
** ''for many Bravais types (defined at [http://www.iucr.org/iucr-top/cif/cifdic_html/2/cif_sym.dic/Ispace_group.Bravais_type.html]), there are several possible point groups (tP and tI: 4, 422; hP: 3, 6, 312, 321, 622; hR: 3, 32; cP, cF and cI: 23 and 432) and thus several possible space groups. In these cases, each point group has to be tested: the SPACE_GROUP_NUMBER has to be changed to one of those consistent with the point group, and the CORRECT step re-run.'' | |||
* ''repeat for each possible lattice character'' | |||
* ''finally decide on the correct Bravais lattice and point group by comparing R-factors (in particular R<sub>meas</sub>), and, from there, come up with possible space groups by looking at the table of systematic absences along the h,0,0 0,k,0 and 0,0,l axes of the diffraction pattern.'' | |||
Be aware of the possibility of [http://www.ccp4.ac.uk/dist/html/twinning.html twinning], and of the different, but equivalent ways to index a given diffraction pattern ([[reindexing]])! | |||
---- | |||
== Example == | |||
old versions of XDS produced a list sorted by Lattice Character number: | |||
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 | ||
Line 49: | Line 79: | ||
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 | ||
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 | ||
Line 64: | Line 94: | ||
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. | |||
== List of Bravais-lattices and their corresponding space group possibilities == | |||
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] |