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3CSL: Difference between revisions
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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. | ||