This is a quick processing overview of P141.  For more detail, please contact the authors

Original processing was done using the cctbx.xfel GUI. See:
http://cci.lbl.gov/publications/download/CCN_2019_p22_Brewster.pdf
Here, command line instructions are given instead. Note, the file paths for the original processing are unchanged in the phil files.

For a given run, say run 47, it can be processed using dials.stills_process:
mpirun dials.still_process data.loc indexing.phil mp.method=mpi

Where data.loc is a file with these lines:
experiment=cxip14117
run=47
detector_address=CxiDs1.0:Cspad.0
cspad.detz_offset=578.0

The indexing phil is provided, which references the provided geometry file (refined_level2_expt0000.expt) and provided mask file (mask.pickle).

An optional ensemble refinement step may be performed for a per-run detector position refinement.  That is done using this command:
cctbx.xfel.stripe_experiment striping.results_dir=/path/to/results striping.trial=XXX striping.run=47 striping.rungroup=YYY striping.stripe=False combine_experiments.clustering.use=False reintegration.integration.summation.detector_gain=25
With additional parameters as needed depending on your computing cluster. The program expects results organized as the XFEL GUI does, namely /path/to/results/r0047/XXX_rgYYY.

Merging was done using cctbx.xfel.merge, documented here:
https://github.com/cctbx/cctbx_project/tree/master/xfel/merging

The command is
mpirun cctbx.xfel.merge merge.phil

It uses the provided merge.phil file, and CRY11B_pH10.4-round10-buster.pdb as a merging reference file.