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Space group determination: Difference between revisions
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=== Space groups as combinations of symmetry elements === | === Space groups as combinations of symmetry elements === | ||
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! Laue group | ! Laue group | ||
! Bravais type | ! Bravais type | ||
! CORRECT | ! spacegroup <br> number <br> suggested by <br> CORRECT | ||
! other possibilities | ! other possibilities | ||
! Comment | ! Comment | ||
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If you find an error in the table please send an email to kay dot diederichs at uni-konstanz dot de ! | If you find an error in the table please send an email to kay dot diederichs at uni-konstanz dot de ! | ||
== The 65 space groups in which proteins composed of L-amino acids can crystallize == | |||
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] | |||
== Space group selected by XDS: ambiguous with respect to enantiomorph and screw axes == | |||
In case of a crystal with an unknown space group (SPACE_GROUP_NUMBER=0 in [[XDS.INP]]), XDS (since [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/Release_Notes.html version June 2008]) helps the user in determination of the correct space group, by suggesting possible space groups compatible with the Laue symmetry and Bravais type of the data, and by calculating the R<sub>meas</sub> for these space groups. | |||
XDS (or rather, the [[CORRECT.LP|CORRECT]] step) makes an attempt to pick the correct space group automatically: it chooses that space group which has the highest symmetry (thus yielding the lowest number of unique reflections) and still a tolerable R<sub>meas</sub> compared to the R<sub>meas</sub> the data have in any space group (which is most likely a low-symmetry space group - often P1). | |||
In some cases the automatic choice is the correct one, and re-running the [[CORRECT.LP|CORRECT]] step is then not necessary. However, neither the correct enantiomorph nor screw axes (see below) are determined automatically by XDS. | |||
== Space group selected by user == | == Space group selected by user == | ||
In case the space group selected by XDS should be incorrect, the resulting list (in CORRECT.LP) should give the user enough information to pick the correct space group herself (alternatives are in the big table above!). The user may then put suitable lines with SPACE_GROUP_NUMBER=, UNIT_CELL_CONSTANTS= into XDS.INP and re-run the CORRECT step to obtain the desired result. (The REIDX= line is no longer required; XDS figures the matrix out.) | |||
== Influencing the selection by XDS == | == Influencing the selection by XDS == | ||
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== Screw axes == | == Screw axes == | ||
The current version makes no attempt to find out about screw axes. It is assumed that the user checks the table in CORRECT.LP entitled | The current version makes no attempt to find out about screw axes. It is assumed that the user checks the table in CORRECT.LP entitled '''REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*)''', and identifies whether the intensities follow the rules | ||
# a two-fold screw axis along an axis in reciprocal space (theoretically) results in zero intensity for the odd-numbered (e.g. 0,K,0 with K = 2*n + 1) reflections, leaving the reflections of type 2*n as candidates for medium to strong reflections (they don't ''have'' to be strong, but they ''may'' be strong!). | # a two-fold screw axis along an axis in reciprocal space (theoretically) results in zero intensity for the odd-numbered (e.g. 0,K,0 with K = 2*n + 1) reflections, leaving the reflections of type 2*n as candidates for medium to strong reflections (they don't ''have'' to be strong, but they ''may'' be strong!). | ||
# similarly, a three-fold screw axis (theoretically) results in zero intensity for the reflections of type 3*n+1 and 3*n+2, and allows possibly strong 3*n reflections . 3<sub>1</sub> and 3<sub>2</sub> cannot be distinguished. | # similarly, a three-fold screw axis (theoretically) results in zero intensity for the reflections of type 3*n+1 and 3*n+2, and allows possibly strong 3*n reflections . 3<sub>1</sub> and 3<sub>2</sub> cannot be distinguished - they are enantiomorphs. | ||
# analogously for four-fold and six-fold axes. | # analogously for four-fold and six-fold axes. | ||
Once screw axes have been deduced from the patterns of intensities along H,0,0 0,K,0 0,0,L , the resulting space group should be identified in the lists of space group numbers printed in IDXREF.LP and CORRECT.LP, and the CORRECT step can be re-run. Those reflections that should theoretically have zero intensity are then marked with a "*" in the table. In practice, they should be (hopefully quite) weak, or even negative. | Once screw axes have been deduced from the patterns of intensities along H,0,0 0,K,0 0,0,L , the resulting space group should be identified in the lists of space group numbers printed in IDXREF.LP and CORRECT.LP, and the CORRECT step can be re-run. Those reflections that should theoretically have zero intensity are then marked with a "*" in the table. In practice, they should be (hopefully quite) weak, or even negative. | ||
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** ambiguity of hand of screw axis (e.g. 3<sub>1</sub> versus 3<sub>2</sub>, or 6<sub>2</sub> versus 6<sub>4</sub>) - see the table above! | ** ambiguity of hand of screw axis (e.g. 3<sub>1</sub> versus 3<sub>2</sub>, or 6<sub>2</sub> versus 6<sub>4</sub>) - see the table above! | ||
** twinning may make a low-symmetry space group look like a high-symmetry one | ** twinning may make a low-symmetry space group look like a high-symmetry one | ||
* [[pointless]] helps with identification of screw axes, and its identification of Laue group is more sensitive than that implemented in CORRECT. However it is not fail-safe, and cannot tell the correct enantiomorph. | |||
* only when the structure is satisfactorily refined can the chosen space group be considered established and correct. Until then, it is just a hypothesis and its alternatives (see the table) should be kept in mind. | * only when the structure is satisfactorily refined can the chosen space group be considered established and correct. Until then, it is just a hypothesis and its alternatives (see the table) should be kept in mind. | ||