Optimisation: Difference between revisions

Optimisation (view source)

Revision as of 13:03, 4 December 2007

55 bytes added , 4 December 2007

m

→‎Final polishing

Kay

Bureaucrats

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edits

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 == Final polishing ==
+=== Re-INTEGATEing with the refined geometry ===
-* After running through all steps of XDS (including space group determination), one might want to
+After running through all steps of XDS (including space group determination), one might want to
   cp GXPARM.XDS XPARM.XDS
   mv CORRECT.LP CORRECT.LP.old
   grep -v REIDX XDS.INP > XDS.INP.new
   mv XDS.INP.new XDS.INP
-:and re-run the INTEGRATE and CORRECT steps. This has the advantage that the refined geometry parameters (from CORRECT) are recycled into INTEGRATE, which sometimes leads to better R-factors.
+and re-run the INTEGRATE and CORRECT steps. This has the advantage that the refined geometry parameters (from CORRECT) are recycled into INTEGRATE, which sometimes leads to better R-factors.
-----
-* Wilson outliers: look through the list of reflections labeled as "aliens" in [[CORRECT.LP]]. Decide whether they follow a slowly decaying non-Wilson distribution (resulting in many reflections with Z > 8 instead of almost none in the case of a Wilson distribution), or whether the top ones are true outliers. The latter occurs most often from ice reflections (these may even be there when no ice rings are visible). <br /> My personal rule of thumb is that when the integer parts of Z ("int(Z)") are the numbers 8, 9, ... n, but there are no aliens (or just a single one) with int(Z) = n+1, then I consider all aliens with Z > n+1 as outliers. A different rule of thumb would be to simply consider aliens with Z of 20 or more as outliers (see [[Wishlist]]). <br /> Outliers should be put (i.e. copied) into REMOVE.HKL, and [[CORRECT]] then should be re-run.<br /> It is useful to inspect the list of aliens after re-running CORRECT; maybe a few more of those should be put into REMOVE.HKL. But this process of rejecting Wilson outliers usually converges very quickly.
+=== Wilson outliers (aliens) ===
+* Look through the list of reflections labeled as "aliens" in [[CORRECT.LP]]. Decide whether they follow a slowly decaying non-Wilson distribution (resulting in many reflections with Z > 8 instead of almost none in the case of a Wilson distribution), or whether the top ones are true outliers. The latter occurs most often from ice reflections (these may even be there when no ice rings are visible). <br /> My personal rule of thumb is that when the integer parts of Z ("int(Z)") are the numbers 8, 9, ... n, but there are no aliens (or just a single one) with int(Z) = n+1, then I consider all aliens with Z > n+1 as outliers. A different rule of thumb would be to simply consider aliens with Z of 20 or more as outliers (see [[Wishlist]]). <br /> Outliers should be put (i.e. copied) into REMOVE.HKL, and [[CORRECT]] then should be re-run.<br /> It is useful to inspect the list of aliens after re-running CORRECT; maybe a few more of those should be put into REMOVE.HKL. But this process of rejecting Wilson outliers usually converges very quickly.
 * Another way to judge Wilson outliers is to identify resolution ranges that deviate from 1. in the table '''HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF ACENTRIC DATA''' in [[CORRECT.LP]]. "Aliens" that are put into REMOVE.HKL will lower the values in these resolution ranges!
 * SCALEPACK users: don't confuse this process of rejecting Wilson outliers with the iterative procedure of rejecting scaling outliers that is usually done when using SCALEPACK. Scaling outliers are handled non-iteratively in [[XDS]]; the only way to influence [[XDS]] in this respect is by modifying [[WFAC1]].