Resolving an Indexing Ambiguity

Here we describe the use of Brehm & Diederichs algorithm 2 to resolve the indexing ambiguity for XFEL data. This is applicable for all polar space groups (where the Bravais symmetry is higher than the space group symmetry) and also for cases with pseudo symmetry (e.g., a monoclinic cell with a near 90-degree beta angle).

Brief Description of the Workflow

It is assumed that the reader is familiar with the tutorial for Merging. The usual workflow of cxi.merge followed by cxi.xmerge will fail in the xmerge step if there are reindexing operators (not H,K,L) that relate the individual indexed lattices to one another. We resolve this by (1) running the cxi.merge step to generate a database with all the observations; (2) use Brehm-Diederichs algorithm 2 to identify the reindexing operators with cxi.brehm_diederichs; (3) re-run the cxi.merge + cxi.xmerge process with the additional list of reindexing operators as input.