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Reindexing: Difference between revisions
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There are two uses of the REIDX= keyword. | There are two uses of the REIDX= keyword. | ||
== Use of REIDX= in [[space group determination]] == | |||
See [[space group determination]]. | |||
== Use of REIDX= for alternative indexing of given diffration pattern == | |||
The other use is in a final step that might have to be done in order to make the reduced data consistent with another existing dataset, or an atomic model. For some background, see [http://www.ccp4.ac.uk/dist/html/reindexing.html reindexing]. The classic description of this is that these are crystals where the Laue symmetry is of a lower order than the apparent crystal lattice symmetry. Unfortunately, however, even P1 crystals can have cells which may be transformed such that the cell parameters are (almost) the same, but the indexing is different. An example is a triclinic cell with parameters a=58.5 b=73.1 c=83.6 alpha=80 beta=70 gamma=89 which gives similar cell parameters under the transformation REIDX=1 0 0 0 0 -1 0 0 1 0 -1 0. | The other use is in a final step that might have to be done in order to make the reduced data consistent with another existing dataset, or an atomic model. For some background, see [http://www.ccp4.ac.uk/dist/html/reindexing.html reindexing]. The classic description of this is that these are crystals where the Laue symmetry is of a lower order than the apparent crystal lattice symmetry. Unfortunately, however, even P1 crystals can have cells which may be transformed such that the cell parameters are (almost) the same, but the indexing is different. An example is a triclinic cell with parameters a=58.5 b=73.1 c=83.6 alpha=80 beta=70 gamma=89 which gives similar cell parameters under the transformation REIDX=1 0 0 0 0 -1 0 0 1 0 -1 0. | ||
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Attention: whenever there is a possibility of alternative indexing, there is also a chance that the crystal (and its data) may be twinned! In the example above, the twinning law is h, -k , h-l . A good tool to identify this situation is [http://www.ccp4.ac.uk/html/sfcheck.html SFCHECK]. Whenever you see '''!!! WARNING !!! SOLUTION MAY NOT BE UNIQUE.''' in IDXREF.LP, you should be aware of this possible problem. | Attention: whenever there is a possibility of alternative indexing, there is also a chance that the crystal (and its data) may be twinned! In the example above, the twinning law is h, -k , h-l . A good tool to identify this situation is [http://www.ccp4.ac.uk/html/sfcheck.html SFCHECK]. Whenever you see '''!!! WARNING !!! SOLUTION MAY NOT BE UNIQUE.''' in IDXREF.LP, you should be aware of this possible problem. | ||
FIXME: shortly discuss merohedral (Laue symmetry is of a lower order than the apparent crystal lattice symmetry) and non-merohedral twinning (example above) here. | FIXME: shortly discuss merohedral (Laue symmetry is of a lower order than the apparent crystal lattice symmetry) and non-merohedral twinning (example above) here. | ||
The two uses of REIDX= outlined above are mutually exclusive: only when the spacegroup is known, it makes sense to test alternative ways of indexing. That means: one ''cannot'' run IDXREF and INTEGRATE with SPACE_GROUP_NUMBER=0, | == Comparing the two uses of REIDX= == | ||
The two uses of REIDX= outlined above are mutually exclusive: only when the spacegroup is known, it makes sense to test alternative ways of indexing. That means: one ''cannot'' run IDXREF and INTEGRATE with SPACE_GROUP_NUMBER=0, '''and also'' try alternative indexing in [[CORRECT]] (unless one does the required matrix multiplication manually). | |||
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