Reindexing: Difference between revisions
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There are two uses of the REIDX= keyword. | |||
The first of these is during [[space group determination]]. | |||
---- | |||
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].) We should rather use the term "alternative indexing" for this mode of reindexing. | |||
The connection between | Possible alternative indexing operators available for this purpose, and consistent with the cell parameters, are listed at the bottom of [[IDXREF.LP]]: | ||
!!! WARNING !!! SOLUTION MAY NOT BE UNIQUE. | |||
OTHER POSSIBLE SOLUTIONS CAN BE TRIED IN THE "CORRECT" STEP | |||
BY USING THE REINDEXING CARDS PRINTED BELOW. | |||
REINDEXING CARD QUALITY | |||
1 1 0 0 0 -1 0 0 0 0 -1 0 0.00 | |||
''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. | |||
---- | |||
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). | |||
---- | |||
To explain in a different way - there are two possible strategies for XDS data reduction: | |||
# 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. | |||
# 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. | |||
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). | |||
Revision as of 14:51, 26 November 2007
There are two uses of the REIDX= keyword.
The first of these is during space group determination.
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 reindexing.) We should rather use the term "alternative indexing" for this mode of reindexing.
Possible alternative indexing operators available for this purpose, and consistent with the cell parameters, are listed at the bottom of IDXREF.LP:
!!! WARNING !!! SOLUTION MAY NOT BE UNIQUE.
OTHER POSSIBLE SOLUTIONS CAN BE TRIED IN THE "CORRECT" STEP
BY USING THE REINDEXING CARDS PRINTED BELOW.
REINDEXING CARD QUALITY
1 1 0 0 0 -1 0 0 0 0 -1 0 0.00
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.
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).
To explain in a different way - there are two possible strategies for XDS data reduction:
- 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.
- 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.
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.
Then the optimization is performed (JOB=INTEGRATE CORRECT) in the correct spacegroup.
After this, one obtains possible reindexing operators (JOB=IDXREF), which may then be tested (JOB=CORRECT).