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It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF: | It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF: | ||
JOB= DEFPIX INTEGRATE CORRECT | |||
Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT. | Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT. | ||
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mv GXPAM.XDS XPARM.XDS | mv GXPAM.XDS XPARM.XDS | ||
and modify XDS.INP to read | and modify XDS.INP to read | ||
JOB= INTEGRATE CORRECT | |||
Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | ||
=== Peak === | === Peak === | ||
360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ | 360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames. | ||
This is an excerpt from [[CORRECT.LP]] : | This is an excerpt from [[CORRECT.LP]] : | ||
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=== High-remote === | === High-remote === | ||
Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ | Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?). | ||
From CORRECT.LP : | From CORRECT.LP : | ||
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=== Inflection === | === Inflection === | ||
360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ | 360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.8 Gb). | ||
CORRECT.LP has: | CORRECT.LP has: | ||
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== Availability of data == | == Availability of data == | ||
There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ | There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [https://{{SERVERNAME}}/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there. | ||
=== additional information for those who want to complete the structure === | === additional information for those who want to complete the structure === |