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| There are two uses of the REIDX= keyword.
| | Use of the REIDX= keyword has been almost completely unnecessary by the "automatic space group determination" performed in the CORRECT step since version June, 2008. |
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| The first of these is during [[space group determination]].
| | An old version of this page (see the history tab) has the text which referred to its use in older versions of XDS. |
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| | == See also == |
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| 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]. Unfortunately, even P1 crystals can have cells which may be transformed such that 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.
| | [[ccp4dev:Reindexing|Reindexing]] in the [[ccp4dev:Main_Page|CCP4 developers' wiki]] |
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| We should rather use the term "alternative indexing" for this mode of reindexing.
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| Possible alternative indexing operators available for this purpose, and consistent with the cell parameters, are listed at the bottom of [[IDXREF.LP]]:
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| !!! WARNING !!! SOLUTION MAY NOT BE UNIQUE.
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| OTHER POSSIBLE SOLUTIONS CAN BE TRIED IN THE "CORRECT" STEP
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| BY USING THE REINDEXING CARDS PRINTED BELOW.
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| REINDEXING CARD QUALITY
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| 1 1 0 0 0 -1 0 0 0 0 -1 0 0.00
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| ''if the [[IDXREF]] step is run in the correct spacegroup''. These operators (usually there's only one) are then applied in the CORRECT step, using the REIDX= keyword and the 12 numbers given. For this to work correctly, INTEGRATE has to use the correct spacegroup, too.
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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 sfcheck. Whenever you see !!! WARNING !!! SOLUTION MAY NOT BE UNIQUE. in IDXREF.LP, you should be aware of this possible problem.
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| 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 ''still'' try alternative indexing in [[CORRECT]] (unless one does the required matrix multiplication manually).
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| To explain in a different way - there are two possible strategies for XDS data reduction:
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| # to use SPACE_GROUP_NUMBER=0 ''up to and including'' INTEGRATE, and to use CORRECT to decide upon the spacegroup with the help of the REIDX= operators from the '''DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE''' table in IDXREF.LP.
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| # to use the known SPACE_GROUP_NUMBER for IDXREF, INTEGRATE and CORRECT. Only using this strategy may alternative indexing possibilities provided by the list '''OTHER POSSIBLE SOLUTIONS CAN BE TRIED ...''' be explored.
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| The connection between these two mutually exclusive strategies is by [[optimization]]: the first pass through the data (JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT) is done to determine the space group, using the first strategy.<br /> Then the [[optimization]] is performed (JOB=INTEGRATE CORRECT) in the correct spacegroup. <br /> After this, one obtains possible reindexing operators (JOB=IDXREF), which may then be tested (JOB=CORRECT).
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