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→IDXREF ends with !!! ERROR !!! message: remedy for case of too short axis, and difference vectors being halved
(→IDXREF ends with !!! ERROR !!! message: remedy for case of too short axis, and difference vectors being halved) |
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JOB= DEFPIX INTEGRATE CORRECT | JOB= DEFPIX INTEGRATE CORRECT | ||
and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES). | and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES). | ||
==== Things to watch out for in IDXREF.LP ==== | |||
The first table "CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS" should show close-to-integer difference vectors. The following is an example how it should ''not'' look like: | |||
# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH | |||
1 -0.0000476-0.0014008-0.0044654 0.0046802 213.67 | |||
2 -0.0101960-0.0056194 0.0019466 0.0118037 84.72 | |||
3 -0.0145331 0.0238225-0.0071754 0.0288134 34.71 | |||
CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS | |||
# COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES | |||
1 0.0004199-0.0012633-0.0043826 2442. 0.97 -0.04 -0.00 | |||
2 0.0101757 0.0060701-0.0019630 2175. -0.03 -1.02 0.01 | |||
3 -0.0076118 0.0114167-0.0040603 1965. 0.13 0.04 0.50 | |||
4 0.0100552 0.0071646 0.0025337 1944. -1.01 -0.99 0.01 | |||
5 0.0072840-0.0101455 0.0084405 1841. -1.10 -0.01 -0.49 | |||
6 0.0000976 0.0027828 0.0089584 1792. -2.00 0.00 -0.00 | |||
7 0.0103103 0.0043851-0.0063902 1790. 0.98 -1.02 0.00 | |||
8 0.0025742 0.0163995-0.0098507 1760. 0.95 -0.99 0.51 | |||
9 0.0068686-0.0089437 0.0128884 1724. -2.08 0.03 -0.49 | |||
10 -0.0174443 0.0123504 0.0161324 1694. -4.01 0.99 0.52 | |||
11 0.0272195-0.0050005-0.0136142 1678. 2.99 -1.97 -0.50 | |||
... | |||
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES) | |||
34.71 84.72 213.67 90.35 90.27 90.06 | |||
This clearly indicates that the third axis above the table (with 1/length=34.71) actually should be twice that size. If this happens, the histogram of indexed spots often has two equally-large subtrees: | |||
SUBTREE POPULATION | |||
1 976 | |||
2 972 | |||
3 10 | |||
4 7 | |||
5 6 | |||
Remedy: take the reduced cell below the table, but double the 34.71, and stick it into the line | |||
UNIT_CELL_CONSTANTS=69.42 84.72 213.67 90.35 90.27 90.06 | |||
To make XDS use that line, specify | |||
SPACE_GROUP_NUMBER=1 | |||
and leave the space group determination for later. | |||
Alternatively, try several well-separated SPOT_RANGEs instead of 1. For example, instead of | |||
SPOT_RANGE=1 900 | |||
try | |||
SPOT_RANGE=1 100 | |||
SPOT_RANGE=801 900 | |||
In most cases, this makes IDXREF pick up the correct cell. | |||
I have seen this working well in many cases of too short cell parameters. | |||
=== IDXREF prints !!! WARNING !!! message === | === IDXREF prints !!! WARNING !!! message === | ||