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Difficult datasets: Difference between revisions
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== optimizing the parameters for INTEGRATE == | == optimizing the parameters for INTEGRATE == | ||
* [http:// | * [http://xds.mpimf-heidelberg.mpg.de/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:// | * [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]= ! do not refine anything in INTEGRATE. This will be very fast and very stable. Very good results are usually obtained with <code>REFINE(INTEGRATE)=POSITION ! maybe add ORIENTATION BEAM</code>; AXIS and CELL should probably not be refined. | ||
* be sure to [[Optimisation#Re-INTEGRATEing_with_the_correct_spacegroup.2C_refined_geometry_and_fine-slicing_of_profiles | recycle]] GXPARM.XDS to XPARM.XDS. | * be sure to [[Optimisation#Re-INTEGRATEing_with_the_correct_spacegroup.2C_refined_geometry_and_fine-slicing_of_profiles | recycle]] GXPARM.XDS to XPARM.XDS. | ||
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or similar. These values then serve as a Bayesian prior for the values that will actually be used for integrating. | or similar. These values then serve as a Bayesian prior for the values that will actually be used for integrating. | ||
If you used larger OSCILLATION_RANGE than 1°, you should increase [http:// | If you used larger OSCILLATION_RANGE than 1°, you should increase [http://xds.mpimf-heidelberg.mpg.de/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 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]]. | 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]]. | ||
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== optimizing the parameters for CORRECT == | == optimizing the parameters for CORRECT == | ||
* [http:// | * [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#NBATCH= NBATCH]= (total angular rotation range)/45 ! to reduce the number of scale factors; the value of NBATCH is shown as NXBIN in CORRECT.LP for the ABSORB and DECAY correction; default is (total angular rotation range)/5. Other values, like (total rotation range)/60 or (total rotation range)/90 might also be tried. Try to match NBATCH with DELPHI (see above). | ||
* maybe [http:// | * maybe [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#CORRECTIONS= CORRECTIONS]= ABSORB ! don't try to correct for MODULATION and DECAY in scaling because these may be poorly determined; however in general it helps to correct for them | ||
* FRIEDEL'S_LAW=TRUE unless there is a known anomalous scatterer. A clear sign that FRIEDEL'S_LAW=TRUE is required is that the CHI^2-VALUE OF FIT OF CORRECTION FACTORS is significantly below 1 (e.g. 0.5). If in doubt use the setting that maximizes ISa. | * FRIEDEL'S_LAW=TRUE unless there is a known anomalous scatterer. A clear sign that FRIEDEL'S_LAW=TRUE is required is that the CHI^2-VALUE OF FIT OF CORRECTION FACTORS is significantly below 1 (e.g. 0.5). If in doubt use the setting that maximizes ISa. | ||