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IDXREF.LP: Difference between revisions
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→Second refinement, after rejecting reflections that do not fit well
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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. | |||