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→Re-INTEGRATEing with the correct spacegroup, refined geometry and fine-slicing of profiles
(paragraph about beam divergence and mosaicity) |
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* read the article [[XDS.INP]] | * read the article [[XDS.INP]] | ||
* for good indexing, follow [[XDS.INP#Keywords which affect whether indexing will succeed]] | * for good indexing, follow [[XDS.INP#Keywords which affect whether indexing will succeed]] | ||
* mask shaded areas of the detector using the UNTRUSTED_RECTANGLE, UNTRUSTED_ELLIPSE and UNTRUSTED_QUADRILATERAL keywords. This is very easy with the [[XDSGUI]] program. | |||
* at least use XDS-Viewer on FRAME.cbf to check the agreement between predicted and observed spots on last frame of dataset. It would be wise to also use XDS-Viewer on MODPIX.cbf and DECAY.cbf to get an impression about systematic effects in your data. | * at least use XDS-Viewer on FRAME.cbf to check the agreement between predicted and observed spots on last frame of dataset. It would be wise to also use XDS-Viewer on MODPIX.cbf and DECAY.cbf to get an impression about systematic effects in your data. | ||
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egrep -v 'JOB|REIDX' XDS.INP > XDS.INP.new | egrep -v 'JOB|REIDX' XDS.INP > XDS.INP.new | ||
echo "! JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT" > XDS.INP | echo "! JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT" > XDS.INP | ||
echo "JOB=INTEGRATE CORRECT" >> XDS.INP | echo "JOB=DEFPIX INTEGRATE CORRECT" >> XDS.INP | ||
echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 >> XDS.INP ! default is 9 | echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 >> XDS.INP ! default is 9 | ||
echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 >> XDS.INP ! default is 9 | echo NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 >> XDS.INP ! default is 9 | ||
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xds_par | xds_par | ||
and thereby 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. It also results in the spacegroup's restraints on the unit cell parameters being used for the prediction of spot positions; these are therefore slightly more accurate. Fine-slicing of profiles has been found to be advantageous at least for Pilatus detectors ([http://dx.doi.org/10.1107/S0907444911049833 Müller, Wang and Schulze-Briese (2012), Acta Cryst D68, 42]), but this should not be specific for Pilatus. | and thereby 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. It also results in the spacegroup's restraints on the unit cell parameters being used for the prediction of spot positions; these are therefore slightly more accurate. Fine-slicing of profiles has been found to be advantageous at least for Pilatus detectors ([http://dx.doi.org/10.1107/S0907444911049833 Müller, Wang and Schulze-Briese (2012), Acta Cryst D68, 42]), but this should not be specific for Pilatus. | ||
You may also want to change the INCLUDE_RESOLUTION_RANGE= line in XDS.INP, in particular to adapt the upper resolution parameter. A very good rule is to set this to the resolution value of the highest shell that still has a "*" appended to the CC1/2 value in [[CORRECT.LP]] . | |||
=== using the refined values for beam divergence and mosaicity for re-integration === | === using the refined values for beam divergence and mosaicity for re-integration === | ||
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* True outliers should be put (i.e. copied) into REMOVE.HKL, and [[CORRECT]] then should be re-run.<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. <br /> A different rule of thumb would be to simply consider aliens with Z of 20 or more as outliers - this is the default since January 2010 (the cutoff may be modified with the REJECT_ALIEN keyword). | * True outliers should be put (i.e. copied) into REMOVE.HKL, and [[CORRECT]] then should be re-run.<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. <br /> A different rule of thumb would be to simply consider aliens with Z of 20 or more as outliers - this is the default since January 2010 (the cutoff may be modified with the REJECT_ALIEN keyword). | ||
* 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! | * 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 | * 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 automatically in [[XDS]] (and [[XSCALE]]); the only way to influence [[XDS]] in this respect is by modifying [[FAQ#reducing_WFAC1_below_its_default_of_1_improves_my_data.2C_right.3F|WFAC1]]. | ||
* if CORRECT rejects many "aliens" in a very weak high resolution shell because they have Z>20 then this is due to the fact that the reflections do not obey Wilson statistics. If this happens, the REJECT_ALIEN parameter should be set much higher (e.g. 100). | |||
=== Optimizing the anomalous signal === | === Optimizing the anomalous signal === | ||
It may be helpful to increase WFAC1 from its default 1.0 to 1.5, to avoid rejection of the strongest Bijvoet pairs (this is not necessary when STRICT_ABSORPTION_CORRECTION=TRUE which is ''not'' the default). | It may be helpful to increase WFAC1 from its default 1.0 to 1.5, to avoid rejection of the strongest Bijvoet pairs (this is not necessary when STRICT_ABSORPTION_CORRECTION=TRUE which is ''not'' the default). | ||
Read [[Tips_and_Tricks#SAD.2FMAD_data_reduction]] concerning STRICT_ABSORPTION_CORRECTION. | Read [[Tips_and_Tricks#SAD.2FMAD_data_reduction]] concerning STRICT_ABSORPTION_CORRECTION. | ||