Difficult datasets - Revision history

Kay: /* optimizing the parameters for DEFPIX */ wording update

2026-03-08T06:31:43Z

optimizing the parameters for DEFPIX: wording update

← Older revision		Revision as of 08:31, 8 March 2026
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	== optimizing the parameters for DEFPIX ==		== optimizing the parameters for DEFPIX ==

	~~For~~ high-resolution data, one ~~probably wants~~ to adjust		Especially for high-resolution data and after inspection of BKGPIX.cbf, one may want to adjust the first automatic masking parameter in
	VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 3000 30000 ! this is used by DEFPIX		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		to a lower value, such that the no pixels at high resolution are considered as shaded due to large background variation. Better to mask with
	UNTRUSTED_RECTANGLE=		UNTRUSTED_RECTANGLE=
	UNTRUSTED_QUADRILATERAL=		UNTRUSTED_QUADRILATERAL=
Line 45:		Line 45:
	grep -v _E.S.D XDS.INP >> x		grep -v _E.S.D XDS.INP >> x
	mv x XDS.INP		mv x XDS.INP
	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. [[XDSGUI]] has a button for this in the ''tools'' menu.

	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 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.
Line 51:		Line 51:
	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]].

	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.		It is important to inspect <code>SHOW_HKL.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 ==

	* [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).		* [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 if few reflections were in the rotation range. The value of NBATCH is shown as NXBIN in CORRECT.LP for the ABSORB and DECAY correction; default is (total angular rotation range)/5. More extreme values, like (total rotation range)/60 or (total rotation range)/90 might also be tried for small molecules. If you changed DELPHI (see above), also change NBATCH according to (total angular rotation range)/DELPHI.
	* 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		* 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 if few reflections were in the rotation range; 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.

Kay: /* optimizing the parameters for IDXREF */

2026-03-07T16:34:22Z

optimizing the parameters for IDXREF

← Older revision		Revision as of 18:34, 7 March 2026
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	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 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 7, 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		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

Kay: fix links

2019-10-22T13:34:04Z

fix links

Kay: /* optimizing the parameters for CORRECT */

2019-08-13T18:19:18Z

optimizing the parameters for CORRECT

← Older revision		Revision as of 20:19, 13 August 2019
Line 57:		Line 57:
	* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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).		* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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		* maybe [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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 ~~the multiplicity~~ is ~~high~~. 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.

	== optimizing the parameters for XSCALE ==		== optimizing the parameters for XSCALE ==

Kay: /* optimizing the parameters for INTEGRATE */

2018-10-12T20:46:34Z

optimizing the parameters for INTEGRATE

← Older revision		Revision as of 22:46, 12 October 2018
Line 35:		Line 35:

	* [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#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. This will be very fast and very stable. Very good results are usually obtained with <code>REFINE(INTEGRATE)=~~ORIENTATION DISTANCE~~ POSITION ! maybe add BEAM</code>; AXIS and CELL should probably 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. 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.

Kay: /* optimizing the parameters for INTEGRATE */

2017-07-03T13:12:52Z

optimizing the parameters for INTEGRATE

← Older revision		Revision as of 15:12, 3 July 2017
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	* [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#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. This will be very fast and very stable. Very good results are usually obtained with <code>REFINE(INTEGRATE)=ORIENTATION DISTANCE POSITION ! maybe add 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.

	Furthermore, you may grab the lines e.g.		Furthermore, you may grab the lines e.g.

Kay: /* optimizing the parameters for COLSPOT */

2017-03-09T10:44:05Z

optimizing the parameters for COLSPOT

← Older revision		Revision as of 12:44, 9 March 2017
Line 5:		Line 5:
	== optimizing the parameters for COLSPOT ==		== optimizing the parameters for COLSPOT ==

	IDXREF depends on the reflection positions stored in SPOT.XDS . This file is written by COLSPOT, and its contents ~~can be~~ visualized e.g. with GNUPLOT:		IDXREF depends on the reflection positions stored in SPOT.XDS . This file is written by COLSPOT, and its contents is visualized in [[XDSGUI]]'s IDXREF tab (or e.g. with GNUPLOT: plot "SPOT.XDS" using 1:2).
	plot "SPOT.XDS" using 1:2
	Obviously, only if the true reflection pattern is represented well by SPOT.XDS can IDXREF be successful. So, play with the following [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html parameters], and use ~~GNUPLOT~~ to find their influence:		Obviously, only if the true reflection pattern is represented well by SPOT.XDS can IDXREF be successful. So, play with the following [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html parameters], and use XDSGUI to find their influence:
	STRONG_PIXEL=		STRONG_PIXEL=
	MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=		MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=

Kay at 10:42, 9 March 2017

2017-03-09T10:42:02Z

← Older revision		Revision as of 12:42, 9 March 2017
Line 11:		Line 11:
	MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=		MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=

	It ~~should be noted that 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.		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 ==

	~~Don~~'t refine ~~the DISTANCE~~ in REFINE(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 ~~60, or even 90~~; 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#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.

Line 35:		Line 48:
	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 ==

Kay: /* optimizing the parameters for CORRECT */

2015-04-29T20:10:16Z

optimizing the parameters for CORRECT

← Older revision		Revision as of 22:10, 29 April 2015
Line 39:		Line 39:
	== optimizing the parameters for CORRECT ==		== optimizing the parameters for CORRECT ==

	* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#NBATCH= NBATCH]= (total 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 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).		* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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		* maybe [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/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 the multiplicity is high. 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 the multiplicity is high. 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.

Kay at 13:37, 8 April 2015

2015-04-08T13:37:26Z

← Older revision		Revision as of 15:37, 8 April 2015
Line 5:		Line 5:
	== optimizing the parameters for COLSPOT ==		== optimizing the parameters for COLSPOT ==

	play with the following [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html parameters], and use GNUPLOT ~~(see below)~~ to find their influence:		IDXREF depends on the reflection positions stored in SPOT.XDS . This file is written by COLSPOT, and its contents can be visualized e.g. with GNUPLOT:
			plot "SPOT.XDS" using 1:2
			Obviously, only if the true reflection pattern is represented well by SPOT.XDS can IDXREF be successful. So, play with the following [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html parameters], and use GNUPLOT to find their influence:
	STRONG_PIXEL=		STRONG_PIXEL=
	MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=		MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=
Line 14:		Line 16:

	Don't refine the DISTANCE in REFINE(IDXREF) !		Don't refine the DISTANCE in REFINE(IDXREF) !

	~~IDXREF depends on the reflection positions stored in SPOT.XDS . This file is written by COLSPOT, and its contents can be visualized e.g. with GNUPLOT:~~
	~~plot "SPOT.XDS" using 1:2~~
	~~Obviously, only if the true reflection pattern is represented well by SPOT.XDS can IDXREF be successful.~~

	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.

← Older revision		Revision as of 15:34, 22 October 2019
Line 34:		Line 34:
	== 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 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://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://~~www~~.mpimf-heidelberg.mpg.de~~/~kabsch/xds~~/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.		* [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://~~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://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://~~www~~.mpimf-heidelberg.mpg.de~~/~kabsch/xds~~/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).		* [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://~~www~~.mpimf-heidelberg.mpg.de~~/~kabsch/xds~~/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		* 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.