Difficult datasets

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
• 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 for CORRECT:

• NBATCH= 4  ! to reduce the number of scale factors; the value of NBATCH is shown as NXBIN in CORRECT.LP for the ABSORB and DECAY correction; default is (total rotation range)/5
• CORRECTIONS= ABSORB  ! don't try to correct for MODULATION and DECAY in scaling

Furthermore, you may try to recycle GXPARM.XDS to XPARM.XDS, and to grab the lines e.g.

BEAM_DIVERGENCE=   2.067  BEAM_DIVERGENCE_E.S.D.=   0.207
REFLECTING_RANGE=  2.303  REFLECTING_RANGE_E.S.D.=  0.329

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.

If you use XSCALE to merge several XDS datasets, you should make sure that you specify in XSCALE.INP the same values for NBATCH and CORRECTIONS as you do, in XDS.INP, for the CORRECT step.