IDXREF.LP - Revision history

Kay: /* A table that rarely occurs: lattices offset from each other in reciprocal space */ correct title

2026-03-13T14:39:23Z

A table that rarely occurs: lattices offset from each other in reciprocal space: correct title

← Older revision		Revision as of 16:39, 13 March 2026
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	The "SPOTS" mentioned above are read from SPOT.XDS, and are collected by COLSPOT. ''Nota bene'': SPOT.XDS is a text file and could be written by a custom program, or a SPOT.XDS written by COLSPOT could be modified afterwards - see [[Indexing]]!		The "SPOTS" mentioned above are read from SPOT.XDS, and are collected by COLSPOT. ''Nota bene'': SPOT.XDS is a text file and could be written by a custom program, or a SPOT.XDS written by COLSPOT could be modified afterwards - see [[Indexing]]!

	== A table that ~~rarely occurs~~: lattices offset from each other in reciprocal space ==		== A table that is only printed if SPACE_GROUP_NUMBER=0: lattices offset from each other in reciprocal space ==
	~~If SPACE_GROUP_NUMBER=0:~~ In case of reflection subsets that are offset from each other by a fractional displacement in reciprocal space, you will then find a table like		In case of reflection subsets that are offset from each other by a fractional displacement in reciprocal space, you will then find a table like
	*** RESULTS FROM LOCAL INDEXING OF 201 DIFFERENCE VECTOR CLUSTERS ***		*** RESULTS FROM LOCAL INDEXING OF 201 DIFFERENCE VECTOR CLUSTERS ***
	MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED 8		MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED 8

Kay: /* A table that rarely occurs: lattices offset from each other in reciprocal space */ wording update

2026-03-07T16:24:10Z

A table that rarely occurs: lattices offset from each other in reciprocal space: wording update

← Older revision		Revision as of 18:24, 7 March 2026
Line 38:		Line 38:

	== A table that rarely occurs: lattices offset from each other in reciprocal space ==		== A table that rarely occurs: lattices offset from each other in reciprocal space ==
	In case of reflection subsets that are offset from each other by a fractional displacement in reciprocal space, you will then find a table like		If SPACE_GROUP_NUMBER=0: In case of reflection subsets that are offset from each other by a fractional displacement in reciprocal space, you will then find a table like
	*** RESULTS FROM LOCAL INDEXING OF 201 DIFFERENCE VECTOR CLUSTERS ***		*** RESULTS FROM LOCAL INDEXING OF 201 DIFFERENCE VECTOR CLUSTERS ***
	MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED 8		MAXIMUM MAGNITUDE OF INDEX DIFFERENCES ALLOWED 8

Kay: /* A table that rarely occurs: lattices offset from each other in reciprocal space */ wording update

2026-03-06T22:09:36Z

A table that rarely occurs: lattices offset from each other in reciprocal space: wording update

← Older revision		Revision as of 00:09, 7 March 2026
Line 55:		Line 55:
	2 29 27949 0.13 -0.43 0.00 0.005978 -0.002899 0.000329 0.006652		2 29 27949 0.13 -0.43 0.00 0.005978 -0.002899 0.000329 0.006652
	3 22 20055 -0.13 0.43 0.00 -0.005989 0.002904 -0.000323 0.006664		3 22 20055 -0.13 0.43 0.00 -0.005989 0.002904 -0.000323 0.006664
	Note: the table shown above was taken from a different dataset than the rest of this article; it is a table ~~occurring in~~ case of [[incommensurate modulation]]!		Note: the table shown above was taken from a different dataset than the rest of this article; it is a table showing a case of [[incommensurate modulation]]!

	== Determination of the reciprocal lattice basis ==		== Determination of the reciprocal lattice basis ==

Kay: table occurring e.g. in case of incommensurate modulation

2026-03-05T11:15:26Z

table occurring e.g. in case of incommensurate modulation

@@ Line 1: / Line 1: @@
-IDXREF.LP is the logfile of the IDXREF "job". It reports on aspects of the analysis of difference vectors, the lattice(s) encountered, their interpretation in terms of 44 Bravais lattices, and the refinement of all geometric parameters of the experiment based on the strong reflections identified in the SPOT_RANGE by COLSPOT.
+IDXREF.LP is the logfile of the [[IDXREF]] "job". It reports on aspects of the analysis of difference vectors, the lattice(s) encountered, their interpretation in terms of 44 Bravais lattices, and the refinement of all geometric parameters of the experiment based on the strong reflections identified in the SPOT_RANGE by COLSPOT.
 In the following, extracts from a typical IDXREF.LP are shown, together with comments, in the order as they occur.
@@ Line 24: / Line 24: @@
   SPACE GROUP AND CELL PARAMETERS ARE UNKNOWN
 The values shown are taken from XDS.INP, or if not given there, the defaults are output.
 "SPACE GROUP AND CELL PARAMETERS ARE UNKNOWN" means that XDS.INP had SPACE_GROUP_NUMBER=0
 == Which data were used for indexing? ==
@@ Line 36: / Line 37: @@
 The "SPOTS" mentioned above are read from SPOT.XDS, and are collected by COLSPOT. ''Nota bene'': SPOT.XDS is a text file and could be written by a custom program, or a SPOT.XDS written by COLSPOT could be modified afterwards - see [[Indexing]]!
 == Determination of the reciprocal lattice basis ==

Kay: /* Determination of the reciprocal lattice basis */

2016-09-09T18:20:28Z

Determination of the reciprocal lattice basis

← Older revision		Revision as of 20:20, 9 September 2016
Line 87:		Line 87:
	From the difference vectors, the "reduced cell" (essentially a P1 cell, with a<b<c) has been established, together with its axes and angles. Furthermore the relation of the reciprocal cell axes (found in the beginning) with respect to the reduced cell is given. If the user supplies UNIT_CELL_CONSTANTS (and SPACE_GROUP_NUMBER >0 ) then these are converted to a reduced cell and given here.		From the difference vectors, the "reduced cell" (essentially a P1 cell, with a<b<c) has been established, together with its axes and angles. Furthermore the relation of the reciprocal cell axes (found in the beginning) with respect to the reduced cell is given. If the user supplies UNIT_CELL_CONSTANTS (and SPACE_GROUP_NUMBER >0 ) then these are converted to a reduced cell and given here.

			'''If the difference vectors are not (close to) integers, something is wrong''' - see [[Problems]].

	== Results from local indexing ==		== Results from local indexing ==

Kay: /* Determination of Bravais lattices consistent with the observed spot positions */

2016-09-09T18:18:19Z

Determination of Bravais lattices consistent with the observed spot positions

← Older revision		Revision as of 20:18, 9 September 2016
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	JOB= DEFPIX INTEGRATE CORRECT		JOB= DEFPIX INTEGRATE CORRECT
	This is a feature (not a bug) to make the user aware of a possible problem.		This is a feature (not a bug) to make the user aware of a possible problem.


			== See also ==

			[[Indexing]]

Kay: /* Determination of Bravais lattices consistent with the observed spot positions */

2012-06-22T00:32:31Z

Determination of Bravais lattices consistent with the observed spot positions

← Older revision		Revision as of 02:32, 22 June 2012
Line 282:		Line 282:
	0.54 1.00		0.54 1.00

	This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap. The maximum oscillation range is less than that given by the table, since the crystal mosaicity has to be subtracted from the table value. Please see [[~~Editing~~ Choice of OSCILLATION RANGE]].		This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap. The maximum oscillation range is less than that given by the table, since the crystal mosaicity has to be subtracted from the table value. Please see [[Choice of OSCILLATION RANGE]].

	cpu time used 2.8 sec		cpu time used 2.8 sec

Kay: /* Determination of Bravais lattices consistent with the observed spot positions */

2012-06-22T00:09:19Z

Determination of Bravais lattices consistent with the observed spot positions

← Older revision		Revision as of 02:09, 22 June 2012
Line 282:		Line 282:
	0.54 1.00		0.54 1.00

	This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap, ~~but it does not take~~ the crystal's mosaicity ~~into account, so one~~ has to ~~subtract~~ the ~~mosaicity (0.1° for good crystals, higher for normal to bad ones)~~. Please ~~note that the resulting value is just the '''maximum value''', ''not'' the '''optimal value'''! A '''good value''', in terms~~ of ~~signal-to-noise ratio, is 0.25-0.5° for CCD detectors, and around 0.1° for the Pilatus. The '''optimal value''' is the ''minimum'' of the '''maximum value''' and the '''good value'''~~.		This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap. The maximum oscillation range is less than that given by the table, since the crystal mosaicity has to be subtracted from the table value. Please see [[Editing Choice of OSCILLATION RANGE]].

	cpu time used 2.8 sec		cpu time used 2.8 sec

Kay: /* Second refinement, after rejecting reflections that do not fit well */

2012-06-20T14:53:40Z

Second refinement, after rejecting reflections that do not fit well

← Older revision		Revision as of 16:53, 20 June 2012
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	Based on the results from the first refinement, all reflections found by COLSPOT are indexed. In this case, a bit more than 1/4 of these are indexed with low error. This leads to the message "!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS" at the bottom of IDXREF.LP , since that fraction is less than [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_FRACTION_OF_INDEXED_SPOTS= MINIMUM_FRACTION_OF_INDEXED_SPOTS] (default 0.50).		Based on the results from the first refinement, all reflections found by COLSPOT are indexed. In this case, a bit more than 1/4 of these are indexed with low error. This leads to the message "!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS" at the bottom of IDXREF.LP , since that fraction is less than [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_FRACTION_OF_INDEXED_SPOTS= MINIMUM_FRACTION_OF_INDEXED_SPOTS] (default 0.50).


			== Determination of Bravais lattices consistent with the observed spot positions ==

			********* DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE *********

			The CHARACTER OF A LATTICE is defined by the metrical parameters of its
			reduced cell as described in the INTERNATIONAL TABLES FOR CRYSTALLOGRAPHY
			Volume A, p. 746 (KLUWER ACADEMIC PUBLISHERS, DORDRECHT/BOSTON/LONDON, 1989).
			Note that more than one lattice character may have the same BRAVAIS LATTICE.

			A lattice character is marked "*" to indicate a lattice consistent with the
			observed locations of the diffraction spots. These marked lattices must have
			low values for the QUALITY OF FIT and their implicated UNIT CELL CONSTANTS
			should not violate the ideal values by more than
			MAXIMUM_ALLOWED_CELL_AXIS_RELATIVE_ERROR= 0.03
			MAXIMUM_ALLOWED_CELL_ANGLE_ERROR= 3.0 (Degrees)

			LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
			CHARACTER LATTICE OF FIT a b c alpha beta gamma

			* 31 aP 0.0 60.8 103.4 132.3 90.0 89.9 89.9
			* 44 aP 0.4 60.8 103.4 132.3 90.0 90.1 90.1
			* 34 mP 2.1 60.8 132.3 103.4 90.0 90.1 90.1
			* 33 mP 2.4 60.8 103.4 132.3 90.0 90.1 90.1
			* 35 mP 3.1 103.4 60.8 132.3 90.1 90.0 90.1
			* 32 oP 3.5 60.8 103.4 132.3 90.0 90.1 90.1
			29 mC 248.7 60.8 215.5 132.3 90.0 90.1 73.7
			28 mC 249.1 60.8 271.5 103.4 90.0 90.1 77.1
			39 mC 250.2 215.5 60.8 132.3 90.1 90.0 73.7
			...
			...

			The above list is sorted by the "Quality of fit" - good values are below 10. Triclinic (Bravais lattice "aP") is always the best since it has no restrictions and can thus most easily fit the reduced cell. The unit cell constants are not cleaned to obey the restrictions, e.g. orthorhombic does not necessarily have alpha=beta=gamma=90°. (Please note that, when specifying unit cell constants in XDS.INP, all restrictions have to be met.)

			For protein crystals the possible space group numbers corresponding to
			each Bravais-type are given below for your convenience. Note, that
			reflection integration is based only on orientation and metric of the
			lattice. It does not require knowledge of the correct space group!
			Thus, if no such information is provided by the user in XDS.INP,
			reflections are integrated assuming a triclinic reduced cell lattice;
			the space group is assigned automatically or by the user in the last
			step (CORRECT) when integrated intensities are available.


			**** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY ****

			BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
			TYPE [SPACE GROUP NUMBER,SYMBOL]
			aP [1,P1]
			mP [3,P2] [4,P2(1)]
			mC,mI [5,C2]
			oP [16,P222] [17,P222(1)] [18,P2(1)2(1)2] [19,P2(1)2(1)2(1)]
			oC [21,C222] [20,C222(1)]
			oF [22,F222]
			oI [23,I222] [24,I2(1)2(1)2(1)]
			tP [75,P4] [76,P4(1)] [77,P4(2)] [78,P4(3)] [89,P422] [90,P42(1)2]
			[91,P4(1)22] [92,P4(1)2(1)2] [93,P4(2)22] [94,P4(2)2(1)2]
			[95,P4(3)22] [96,P4(3)2(1)2]
			tI [79,I4] [80,I4(1)] [97,I422] [98,I4(1)22]
			hP [143,P3] [144,P3(1)] [145,P3(2)] [149,P312] [150,P321] [151,P3(1)12]
			[152,P3(1)21] [153,P3(2)12] [154,P3(2)21] [168,P6] [169,P6(1)]
			[170,P6(5)] [171,P6(2)] [172,P6(4)] [173,P6(3)] [177,P622]
			[178,P6(1)22] [179,P6(5)22] [180,P6(2)22] [181,P6(4)22] [182,P6(3)22]
			hR [146,R3] [155,R32]
			cP [195,P23] [198,P2(1)3] [207,P432] [208,P4(2)32] [212,P4(3)32]
			[213,P4(1)32]
			cF [196,F23] [209,F432] [210,F4(1)32]
			cI [197,I23] [199,I2(1)3] [211,I432] [214,I4(1)32]

			This is just the mapping from Bravais lattice to possible spacegroups.

			Maximum oscillation range to prevent angular overlap at high resolution limit
			assuming zero (!) mosaicity.
			Maximum oscillation range High resolution limit
			(degrees) (Angstrom)
			2.15 4.00
			1.61 3.00
			1.07 2.00
			0.54 1.00

			This is just a little help to tell the user how big the OSCILLATION_RANGE can be without producing overlap, but it does not take the crystal's mosaicity into account, so one has to subtract the mosaicity (0.1° for good crystals, higher for normal to bad ones). Please note that the resulting value is just the '''maximum value''', ''not'' the '''optimal value'''! A '''good value''', in terms of signal-to-noise ratio, is 0.25-0.5° for CCD detectors, and around 0.1° for the Pilatus. The '''optimal value''' is the ''minimum'' of the '''maximum value''' and the '''good value'''.

			cpu time used 2.8 sec
			elapsed wall-clock time 1.7 sec
			!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS
			AUTOMATIC DATA PROCESSING STOPPED. AS THE CRITERIA FOR A GOOD
			SOLUTION ARE RATHER STRICT, YOU MAY CHOOSE TO CONTINUE DATA
			PROCESSING AFTER CHANGING THE "JOB="-CARD IN "XDS.INP" TO
			"JOB= DEFPIX INTEGRATE CORRECT".
			IF THE BEST SOLUTION IS REALLY NONSENSE YOU SHOULD FIRST HAVE
			A LOOK AT THE ASCII-FILE "SPOT.XDS". THIS FILE CONTAINS THE
			INITIAL SPOT LIST SORTED IN DECREASING SPOT INTENSITY. SPOTS
			NEAR THE END OF THE FILE MAY BE ARTEFACTS AND SHOULD BE ERASED.
			ALTERNATIVELY YOU MAY TRY DIFFERENT VALUES FOR "INDEX_ORIGIN"
			AS SUGGESTED IN THE ABOVE LISTING.
			IF THE CRYSTAL HAS SLIPPED AT THE BEGINNING OF DATA COLLECTION
			YOU MAY CHOOSE TO SKIP SOME OF THE FIRST FRAMES BY CHANGING
			THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.

			End of IDXREF.LP. In this case XDS would not automatically continue with the DEFPIX step. Rather, the user has to explicitly state that s/he wants to do this, by changing the JOB line in XDS.INP to
			JOB= DEFPIX INTEGRATE CORRECT
			This is a feature (not a bug) to make the user aware of a possible problem.

Kay: /* Second refinement, after rejecting reflections that do not fit well */

2012-06-19T20:58:23Z

Second refinement, after rejecting reflections that do not fit well

← Older revision		Revision as of 22:58, 19 June 2012
Line 200:		Line 200:
	SPACE GROUP NUMBER 1		SPACE GROUP NUMBER 1

	Based on the results from the first refinement, all reflections found by COLSPOT are indexed. In this case, a bit more than 1/4 of these are indexed with low error. This leads to the message "!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS" at the bottom of IDXREF.LP .		Based on the results from the first refinement, all reflections found by COLSPOT are indexed. In this case, a bit more than 1/4 of these are indexed with low error. This leads to the message "!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 50%) OF INDEXED REFLECTIONS" at the bottom of IDXREF.LP , since that fraction is less than [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#MINIMUM_FRACTION_OF_INDEXED_SPOTS= MINIMUM_FRACTION_OF_INDEXED_SPOTS] (default 0.50).