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Problems: Difference between revisions
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→IDXREF prints !!! WARNING !!! message
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THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN. | THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN. | ||
This is printed out for you to actually read, and take action accordingly. In most cases you just change the | This is printed out for you to actually read, and take action accordingly. In most cases you just change the JOB= line in XDS.INP to read | ||
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). | ||
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If this does not help, try to refine even less items, e.g. leave out AXIS. | If this does not help, try to refine even less items, e.g. leave out AXIS. | ||
=== IDXREF prints ERROR IN REFINE !!! RETURN CODE IS IER= 0 === | |||
This is due to either wrong inputs in XDS.INP, or due to bad data, e.g. spots from many crystals whose diffraction patterns overlap. The first possibility applies if the diffraction pattern is clean. The second applies if the diffraction pattern is ugly, and unsuitable for indexing. In that case, maybe try a different SPOT_RANGE. | |||
=== IDXREF.LP does not show the expected lattice === | === IDXREF.LP does not show the expected lattice === | ||
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BEAM_DIVERGENCE= BEAM_DIVERGENCE_E.S.D.= | BEAM_DIVERGENCE= BEAM_DIVERGENCE_E.S.D.= | ||
then you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have | then there are two ways to resolve this: | ||
* you could insert a line DELPHI=10 (or DELPHI=20, for 10 or 20 degrees batches; the default is 5 degree batches) into XDS.INP and re-run INTEGRATE | |||
* as the error message suggests, you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have | |||
DATA_RANGE=1 135 | DATA_RANGE=1 135 | ||
JOB=INTEGRATE CORRECT | JOB=INTEGRATE CORRECT | ||
Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.) | Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.) | ||
BEAM_DIVERGENCE= 0.478 BEAM_DIVERGENCE_E.S.D.= 0.048 | BEAM_DIVERGENCE= 0.478 BEAM_DIVERGENCE_E.S.D.= 0.048 | ||
REFLECTING_RANGE= 1.100 REFLECTING_RANGE_E.S.D.= 0.157 | REFLECTING_RANGE= 1.100 REFLECTING_RANGE_E.S.D.= 0.157 | ||
Copy them to XDS.INP. Restore the original DATA_RANGE and continue. | Copy them to XDS.INP. Restore the original DATA_RANGE and continue. | ||
If this problem happens with multiple XDS jobs working on the same data set, you might also get a message like | |||
.../bin1_02.tmp | |||
Image PC Routine Line Source | |||
xds_par 0000000000592B91 Unknown Unknown Unknown | |||
xds_par 00000000004BEF21 joinintegrate_ 8995 MAIN_XDS.f90 | |||
xds_par 0000000000410A5B xds_ 21690 MAIN_XDS.f90 | |||
xds_par 000000000040B3A4 MAIN__ 1 MAIN_XDS.f90 | |||
xds_par 00000000004083F6 Unknown Unknown Unknown | |||
libc.so.6 00007FB40222E830 Unknown Unknown Unknown | |||
xds_par 00000000004082E9 Unknown Unknown Unknown | |||
which looks like a real crash of the program, but in this case with a known reason. | |||
Another error mode of INTEGRATE (in processing of small-molecule data) is ... | Another error mode of INTEGRATE (in processing of small-molecule data) is ... | ||
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The error message is misleading in this case: there are too few reflections to build the average profile. The fix is: restart INTEGRATE after inserting e.g. | The error message is misleading in this case: there are too few reflections to build the average profile. The fix is: restart INTEGRATE after inserting e.g. | ||
DELPHI=20 ! default is 5, so try with e.g. 10, 20, 45, 90, 180 | DELPHI=20 ! default is 5, so try with e.g. 10, 20, 45, 90, 180 | ||
and re-run INTEGRATE. | in XDS.INP and re-run INTEGRATE. | ||
=== INTEGRATE cell and/or distance run away; xds crashes or has to be killed === | === INTEGRATE cell and/or distance run away; xds crashes or has to be killed === | ||