3CSL: Difference between revisions

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Revision as of 17:54, 10 February 2011

534 bytes added , 10 February 2011

→‎XDS data reduction of high-remote, peak and inflection

Kay

Bureaucrats

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 The other thing that you might want to try yourself, or just fill in, is
   VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=8000. 30000. ! often 8000 is ok
-instead of the the default (7000. 30000.). This gives a good mask for the beamstop shadow.
+instead of the the default (7000. 30000.). This results in a good mask for the beamstop shadow.
-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. After that,
+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:
+ JOBS= 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.
+Optimization: after this first data reduction pass, I use the "post-refined" geometric parameters, and the correct spacegroup (as given in CORRECT.LP, and written to GXPARM.XDS), for a second pass. Thus I need to
   mv GXPAM.XDS XPARM.XDS
-and another (optimized) integration pass should be performed, after setting
+and modify XDS.INP to read
   JOBS= INTEGRATE CORRECT
-This second pass proceeds in the correct spacegroup (22) which was identified by CORRECT at the end of the first pass.
+Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps.
 === High-remote ===