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Difficult datasets: Difference between revisions
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The following suggestions apply not only to small-molecule datasets, but also to very weak or low-resolution, or otherwise difficult macromolecular datasets. | |||
These datasets have few (or few strong) reflections per frame. Therefore, the multitude of parameters describing the diffraction experiment needs to be reduced (in refinement one would say: to avoid overfitting). This means that e.g. the following parameters may need adjustment (typical values are given): most importantly for INTEGRATE: | |||
* DELPHI=45 ! to base reflection profiles and refinements on more reflections - try this first if yo get error messages in the INTEGRATE step | * DELPHI=45 ! to base reflection profiles and refinements on more reflections - try this first if yo get error messages in the INTEGRATE step | ||
* REFINE(INTEGRATE)= ! do not refine anything in INTEGRATE; be sure to recycle GXPARM.XDS to XPARM.XDS. Also try REFINE(INTEGRATE)=ORIENTATION CELL ! maybe add BEAM, but probably AXIS or DISTANCE should not be refined. | |||
and you may also try | and you may also try for CORRECT: | ||
* NBATCH=4 ! to reduce the number of scale factors | * NBATCH=4 ! to reduce the number of scale factors | ||
* CORRECTIONS= ABSORB ! don't try to correct for MODULATION and DECAY in scaling | * CORRECTIONS= ABSORB ! don't try to correct for MODULATION and DECAY in scaling | ||
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BEAM_DIVERGENCE= 2.067 BEAM_DIVERGENCE_E.S.D.= 0.207 | BEAM_DIVERGENCE= 2.067 BEAM_DIVERGENCE_E.S.D.= 0.207 | ||
REFLECTING_RANGE= 2.303 REFLECTING_RANGE_E.S.D.= 0.329 | REFLECTING_RANGE= 2.303 REFLECTING_RANGE_E.S.D.= 0.329 | ||
from INTEGRATE.LP and to insert them into XDS.INP . | from INTEGRATE.LP and to insert them into XDS.INP . The latter is accomplished easily with | ||
grep _E INTEGRATE.LP | tail -2 > x | |||
grep -v _E.S.D XDS.INP >> x | |||
mv x XDS.INP | |||
or similar. | |||