There is a variety of settings one can change to help situations where the indexing is problematic. Those would be given on the command-line, as in
% process par="val" ...
The parameter
XdsOptimizeIdxrefAlways=yes
will enforce running the "run_idxref" tool even if the initial indexing used a reasonable fraction of all found spots. This can improve indexing by either discarding spots from additional lattices (e.g. in case of a split crystal or if there is radiation damage resulting in a cell parameter drift) or because it is allowed to truly lock into the main solution.
NOTE: this is the default from June 2015 onward.
This can be done semi-automatic with something like
XdsSpotSearchNumImages=20 XdsSpotSearchAngularRange=90 XdsSpotSearchNumRanges=4
which would select a maximum of 20 images in 4 parts from images covering the first 90 degree of data.
One can also explicitly specify the images to use for spot search via e.g.
autoPROC_XdsKeyword_SPOT_RANGE="1 10|91 100"
to use images 1-10 and 91-100.
If there are significant amount of ice-ring spots on the images, the setting of
RunIdxrefExcludeIceRingShells=yes
will remove spots within typical ice-ring resolutions (up to 1.123 A) before going into iterative indexing to get the best solution.
The iterative indexing will by default pick the solution with the most spots indexed. To select a specific solution, use e.g.
XdsOptimizeIdxrefPickSolution=02
which will pick the second solution (note the 2-digit specification).
To use only the strongest spots:
RunIdxrefStartWithTop=1000
which will use the top 1000 spots.
Setting
autoPROC_XdsKeyword_REFINEIDXREF="POSITION CELL AXIS BEAM ORIENTATION"
will switch on distance (POSITION) refinement already at the IDXREF stage. The default for recent XDS versions is to keep the distance fixed (assuming that the header value is accurate).
