Reindexing: Difference between revisions

Reindexing (view source)

Revision as of 14:51, 26 November 2007

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-For some background, see [http://www.ccp4.ac.uk/dist/html/reindexing.html reindexing]
+There are two uses of the REIDX= keyword.
-Reindexing within XDS is 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.
+The first of these is during [[space group determination]].
-Possible reindexing operators are listed at the bottom of [[IDXREF.LP]]
+----
-FIXME: insert example here
-''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.
-Thus there are two possible strategies for XDS data reduction:
+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.
-# 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 table in IDXREF.LP.
-# to use the known SPACE_GROUP_NUMBER for IDXREF, INTEGRATE and CORRECT.
-The connection between the two philosophies is by [[optimization]]: the first pass through the data (JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT) is done to determine the space group. Then the [[optimization]] is performed (JOB=INTEGRATE CORRECT). After this, one obtains possible reindexing operators (JOB=IDXREF), which may then be tested (JOB=CORRECT).
+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  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).