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Difficult datasets: Difference between revisions
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MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= | MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= | ||
It | It is important to correctly mask any shadowed areas on the detector; if not done properly, the variation at the edges will lead to spurious "spots" being picked up by COLSPOT. | ||
== optimizing the parameters for IDXREF == | == optimizing the parameters for IDXREF == | ||
For low-resolution (macromolecular) data, don't refine POSITION (i.e. detector distance) in REFINE(IDXREF) ! This is also what [[generate_XDS.INP]] defaults to, and produces very stable indexing - however, if the distance is not accurate, one needs a second ([[optimisation]]) pass. | |||
For close reflections, you may want to reduce SEPMIN below its default of 6, and set CLUSTER_RADIUS to half of the new value. | For close reflections, you may want to reduce SEPMIN below its default of 6, and set CLUSTER_RADIUS to half of the new value. | ||
For high-resolution (e.g. small molecule) data, do refine POSITION (i.e. detector distance) in REFINE(IDXREF). So you must change XDS.INP w.r.t. what [[generate_XDS.INP]] produces. For such datasets one also wants to set | |||
TEST_RESOLUTION_RANGE=10. 1. | |||
== optimizing the parameters for DEFPIX == | |||
For high-resolution data, one probably wants to adjust | |||
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 3000 30000 ! this is used by DEFPIX | |||
because the variation in background is usually large. Better to mask with | |||
UNTRUSTED_RECTANGLE= | |||
UNTRUSTED_QUADRILATERAL= | |||
UNTRUSTED_ELLIPSE= | |||
which is easily done using [[XDSGUI]]. | |||
== optimizing the parameters for INTEGRATE == | == optimizing the parameters for INTEGRATE == | ||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI]=45 ! (or | * [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI]=45 ! (or some multiple of 15; the default is 5) to base reflection profiles and refinements on more reflections - try this first if you get error messages about incomplete profiles or failure to allocate memory in the INTEGRATE step, or if the geometric parameters during INTEGRATE refinements "run away" | ||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]= ! do not refine anything in INTEGRATE; be sure to [[Optimisation#Re-INTEGRATEing_with_the_correct_spacegroup.2C_refined_geometry_and_fine-slicing_of_profiles | recycle]] GXPARM.XDS to XPARM.XDS. Also try REFINE(INTEGRATE)=ORIENTATION DISTANCE ! maybe add BEAM, but probably AXIS or CELL should not be refined. | * [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]= ! do not refine anything in INTEGRATE; be sure to [[Optimisation#Re-INTEGRATEing_with_the_correct_spacegroup.2C_refined_geometry_and_fine-slicing_of_profiles | recycle]] GXPARM.XDS to XPARM.XDS. Also try REFINE(INTEGRATE)=ORIENTATION DISTANCE ! maybe add BEAM, but probably AXIS or CELL should not be refined. | ||
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If you used larger OSCILLATION_RANGE than 1°, you should increase [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_ERROR_OF_SPINDLE_POSITION= MAXIMUM_ERROR_OF_SPINDLE_POSITION=] (default is 2°) because you expect larger deviations of experimentally determined and calculated phi positions of reflections. Same might apply to MAXIMUM_ERROR_OF_SPOT_POSITION= ; the default is 3 pixels which may be too low to account for broad reflections. If you don't do this, many reflections that violate these limits will not be used for geometry refinement, which may turn out to be unstable. | If you used larger OSCILLATION_RANGE than 1°, you should increase [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_ERROR_OF_SPINDLE_POSITION= MAXIMUM_ERROR_OF_SPINDLE_POSITION=] (default is 2°) because you expect larger deviations of experimentally determined and calculated phi positions of reflections. Same might apply to MAXIMUM_ERROR_OF_SPOT_POSITION= ; the default is 3 pixels which may be too low to account for broad reflections. If you don't do this, many reflections that violate these limits will not be used for geometry refinement, which may turn out to be unstable. | ||
If your crystal diffracts to high angles (e.g. small molecules) then the absorption in the detector surface affects both position and intensity of the recorded x-rays. XDS has two parameters, SENSOR_THICKNESS and [[SILICON]], to take care of that. If the data are measured with a Pilatus detector, the defaults are ok. If however a CCD is used then both SENSOR_THICKNESS and SILICON should be adjusted manually - see [[SILICON]]. | If your crystal diffracts to high angles (e.g. small molecules) then the absorption in the detector surface affects both position and intensity of the recorded x-rays. XDS has two parameters, SENSOR_THICKNESS and [[SILICON]], to take care of that. If the data are measured with a Pilatus or Eiger detector, the defaults are ok. If however a CCD is used then both SENSOR_THICKNESS and SILICON should be adjusted manually - see [[SILICON]]. | ||
It is important to inspect <code>FRAME.cbf</code> after the XDS run. This will reveal problems e.g. with masking of shadows and additional lattices. | |||
== optimizing the parameters for CORRECT == | == optimizing the parameters for CORRECT == | ||