What options do I have for cases with difficult indexing?

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" ...

Allow iterative indexing

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.

Specify a different range of images to use for spot-search

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 explicitely 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.

Remove ice-rings before indexing

If there are significant amount of ice-ring spots on the images, the combination of

XdsOptimizeIdxrefAlways=yes
RunIdxrefExcludeIceRingShells=yes

will remove spots within typical ice-ring resolutions (3.90, 3.67, 3.44, 2.67, 2.25, 2.07, 1.95, 1.92, 1.88 and 1.72 A) before going into iterative indexing to get the best solution.

Picking a specific solution from iterative indexing

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).

Use only the strongest spots for indexing

To use only the strongest spots:

XdsOptimizeIdxrefAlways=yes
RunIdxrefStartWithTop=1000

which will use the top 1000 spots.