2,684
edits
Space group determination: Difference between revisions
Jump to navigation
Jump to search
→An example
(→Notes) |
|||
| Line 186: | Line 186: | ||
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. <code>[[pointless]] XDS_ASCII.HKL</code> gives: | ||
<pre> | |||
Analysing rotational symmetry in lattice group I 4/m m m | |||
---------------------------------------------- | |||
<!--SUMMARY_BEGIN--> | |||
Scores for each symmetry element | |||
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell) | |||
1 0.856 7.77 0.78 9368 0.224 identity | |||
2 0.139 2.98 0.30 6376 0.894 2-fold l ( 0 0 1) {-h,-k,l} | |||
3 0.842 8.02 0.80 18679 0.234 ** 2-fold k ( 0 1 0) {-h,k,-l} | |||
4 0.148 3.10 0.31 5858 1.254 2-fold h ( 1 0 0) {h,-k,-l} | |||
5 0.073 1.25 0.13 12111 1.077 2-fold ( 1-1 0) {-k,-h,-l} | |||
6 0.071 1.11 0.11 12293 1.152 2-fold ( 1 1 0) {k,h,-l} | |||
7 0.068 0.83 0.08 24758 1.084 4-fold l ( 0 0 1) {-k,h,l}{k,-h,l} | |||
</pre> | |||
and this shows that actually there is only one instead of three two-fold axes, despite the fact that CORRECT auto-chose the orthorhombic system and possibly even rejected some reflections that do not fit it well. | |||
Pointless then re-indexes to I2 and suggests: | |||
<pre> | |||
Best Solution: space group I 1 2 1 | |||
Reindex operator: [h,k,l] | |||
Laue group probability: 0.763 | |||
Systematic absence probability: 1.000 | |||
Total probability: 0.763 | |||
Space group confidence: 0.687 | |||
Laue group confidence 0.687 | |||
Unit cell: 78.05 80.78 235.63 90.00 90.00 90.00 | |||
50.67 to 3.73 - Resolution range used for Laue group search | |||
50.67 to 3.08 - Resolution range in file, used for systematic absence check | |||
Number of batches in file: 120 | |||
The data do not appear to be twinned, from the L-test | |||
$$ <!--SUMMARY_END--> | |||
HKLIN spacegroup: I 2 2 2 body-centred orthorhombic | |||
$TEXT:Warning:$$ $$ | |||
The input crystal system is body-centred orthorhombic | |||
(Cell: 78.05 80.78 235.63 90.00 90.00 90.00) | |||
The crystal system chosen for output is body-centred monoclinic | |||
(Cell: 78.05 80.78 235.63 90.00 90.00 90.00) | |||
$TEXT:Warning:$$ $$ | |||
WARNING: | |||
WARNING: | |||
The chosen output crystal system is different from that used for integration of the input file(s). | |||
You should rerun the integration in the chosen crystal system because the cell constraints differ | |||
$$ | |||
Filename: | |||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |||
Final point group choice has alternative indexing possibilities | |||
Alternative indexing possibilities are marked '*' if the cells are | |||
too different at the maximum resolution | |||
CellDifference(A) ReindexOperator | |||
1 0.0 [h,k,l] | |||
2 0.0 [h,-k,-l] | |||
3 8.0 * [k,-h,l] | |||
4 8.0 * [-k,h,l] | |||
</pre> | |||
At the bottom of the output, we see that other indexing possibilities exist. That means that one has to be very careful when merging crystals from this project, and that there may also be the possibility of twinning. | |||
In this particular case, CORRECT chose the wrong symmetry and 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. | |||
Important note: pointless should really be run with the "SETTING SYMMETRY-BASED" option. When doing that, the output changes to | |||
<pre> | |||
Best Solution: space group C 1 2 1 | |||
Reindex operator: [h+l,k,-h] | |||
Laue group probability: 0.807 | |||
Systematic absence probability: 1.000 | |||
Total probability: 0.807 | |||
Space group confidence: 0.734 | |||
Laue group confidence 0.734 | |||
Unit cell: 248.53 80.86 78.08 90.00 108.31 90.00 | |||
40.76 to 3.80 - Resolution range used for Laue group search | |||
40.76 to 3.08 - Resolution range in file, used for systematic absence check | |||
Number of batches in file: 120 | |||
The data do not appear to be twinned, from the L-test | |||
$$ <!--SUMMARY_END--> | |||
HKLIN spacegroup: I 2 2 2 body-centred orthorhombic | |||
$TEXT:Warning:$$ $$ | |||
The input crystal system is body-centred orthorhombic | |||
(Cell: 78.08 80.86 235.95 90.00 90.00 90.00) | |||
The crystal system chosen for output is C-centred monoclinic | |||
(Cell: 248.53 80.86 78.08 90.00 108.31 90.00) | |||
$TEXT:Warning:$$ $$ | |||
WARNING: | |||
WARNING: | |||
The chosen output crystal system is different from that used for integration of the input file(s). | |||
You should rerun the integration in the chosen crystal system because the cell constraints differ | |||
$$ | |||
</pre> | |||
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. | |||
Another note: 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 correct unit cell: | |||
<pre> | |||
SPACE_GROUP_NUMBER=1 | |||
UNIT_CELL_CONSTANTS= 74.1 78.6 124.0 108.2 105.2 90.4 | |||
</pre> | |||
in XDS.INP and re-runs CORRECT. That gives an unbiased XDS_ASCII.HKL. In this case though, the output of pointless is practically unchanged, whether XDS_ASCII.HKL was scaled in oI (=22 or 23) or P1.. | |||