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Space group determination: Difference between revisions
→An example
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</pre> | </pre> | ||
The automatic choice gave 23 as a result. This is because the associated R<sub>meas</sub> (39.5) is lower than MAX_FAC_RMEAS * (lowest R<sub>meas</sub>) = 2 * 22.5 = 45.0. | The automatic choice gave 23 as a result. This is because the associated R<sub>meas</sub> (39.5) is lower than MAX_FAC_RMEAS * (lowest R<sub>meas</sub>) = 2 * 22.5 = 45.0. | ||
However, the C2 values of 30.7 and 31.0 are significantly lower still, and the question needs further investigation. <code>[[pointless]] XDS_ASCII.HKL</code> gives: | However, the C2 values of 30.7 and 31.0 are significantly lower still, and the question needs further investigation. | ||
=== checking the CORRECT assignment with [[pointless]] === | |||
<code>[[pointless]] XDS_ASCII.HKL</code> gives: | |||
<pre> | <pre> | ||
Analysing rotational symmetry in lattice group I 4/m m m | Analysing rotational symmetry in lattice group I 4/m m m | ||
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In this particular case, CORRECT chose the wrong symmetry, whereas pointless identified the correct symmetry elements. I have also seen cases where pointless mis-identified the symmetry, usually on the side of too high symmetry. To avoid mistakes in space group identification, it is absolutely crucial to read and understand the tables that the programs print. | In this particular case, CORRECT chose the wrong symmetry, whereas pointless identified the correct symmetry elements. I have also seen cases where pointless mis-identified the symmetry, usually on the side of too high symmetry. To avoid mistakes in space group identification, it is absolutely crucial to read and understand the tables that the programs print. | ||
=== a more sensible way to run pointless === | |||
pointless should really be run with the "SETTING SYMMETRY-BASED" option. When doing that, the output changes to | |||
<pre> | <pre> | ||
Best Solution: space group C 1 2 1 | Best Solution: space group C 1 2 1 | ||
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so the spacegroup given is the more normal C2 setting (instead of A2 or I2). Unfortunately, pointless does not seem to print out the table of "alternative indexing possibilities" in this mode - but possibly the table is only printed in the I2 case because the beta angle comes out as 90.0°. | so the spacegroup given is the more normal C2 setting (instead of A2 or I2). Unfortunately, pointless does not seem to print out the table of "alternative indexing possibilities" in this mode - but possibly the table is only printed in the I2 case because the beta angle comes out as 90.0°. | ||
=== not biasing the cell parameters, and avoiding premature outlier rejection === | |||
CORRECT can easily be forced ''not'' to assign a spacegroup, and consequently will not reject outliers based on a too high symmetry assignment. To this end one simply supplies space group P1 and its unit cell: | |||
<pre> | <pre> | ||
SPACE_GROUP_NUMBER=1 | SPACE_GROUP_NUMBER=1 | ||
UNIT_CELL_CONSTANTS= 74.1 78.6 124.0 108.2 105.2 90.4 | UNIT_CELL_CONSTANTS= 74.1 78.6 124.0 108.2 105.2 90.4 | ||
</pre> | </pre> | ||
in XDS.INP and re-runs CORRECT. That gives an unbiased XDS_ASCII.HKL. | in XDS.INP and re-runs CORRECT. That gives an unbiased XDS_ASCII.HKL, with no angles set to 90°. pointless ''with'' SETTING SYMMETRY_BASED then gives | ||
<pre> | |||
Best Solution: space group C 1 2 1 | |||
Reindex operator: [-k-2l,-k,-h] | |||
Laue group probability: 0.849 | |||
Systematic absence probability: 1.000 | |||
Total probability: 0.849 | |||
Space group confidence: 0.770 | |||
Laue group confidence 0.770 | |||
Unit cell: 233.70 78.42 73.22 90.31 105.34 89.77 | |||
<pre> | |||
and ''without'' | |||
<pre> | |||
Best Solution: space group I 1 2 1 | |||
Reindex operator: [-h,-k,h+k+2l] | |||
Laue group probability: 0.838 | |||
Systematic absence probability: 1.000 | |||
Total probability: 0.838 | |||
Space group confidence: 0.753 | |||
Laue group confidence 0.753 | |||
Unit cell: 233.70 78.42 73.22 90.31 105.34 89.77 | |||
</pre> | |||
the dreadful I2 space group nomenclature (and I have no idea why the probability and confidence values are worse than in C2). But anyway this shows that there are two non-equivalent ways to index the same lattice! | |||
=== final steps === | |||
Finally, XDS (but only JOB=DEFPIX INTEGRATE CORRECT) should be re-run with | |||
<pre> | |||
SPACE_GROUP_NUMBER=5 | |||
UNIT_CELL_CONSTANTS= 233.70 78.42 73.22 90.31 105.34 89.77 | |||
</pre> | |||
because this enforces just the correct cell constraints. | |||