This dataset consists of two sets of runs:

MCR_BS_Ni1_c125_1.55_remerge (PDBID 9N46): runs 270-279, 282-284, 286-290, 293-294, 297
MCR_BS_Ni2_123c_cut1.50A_main (PDBID 9MVN): runs 298-302

These runs are stored as XTC streams and require the LCLS specifc library psana.  To process the data, first set up your environment according to
https://github.com/cctbx/cctbx_project/tree/master/xfel/conda_envs#lcls-environment

DIALS interacts with psana through locator files.  The locator folder contains the locator files for these runs, and in them you can see beam calibration and detector information.

Data were indexed using cctbx.xfel in the cctbx.xfel GUI.  To reproduce on the command lind, use dials.stills_process as so:

dials.stills_process <path to locator file> input_files/index.phil

Note: adjust the paths in index.phil appropiately.
Note: for runs 297-302, dials.stills_process was ran with the additional parameter indexing.stills.method_list="fft1d fft3d"

From here, time dependent ensemble refinement was applied using the XFEL GUI, not reproduced here.

Merging was done as follows:

cctbx.xfel.merge MCR_BS_Ni1_c125_merge.phil
and
cctbx.xfel.merge MCR_BS_Ni2_123c_merge.phil

Again, take care to adjust the paths in the phil files.

Note the covariance files used during merging are generated using the cctbx.xfel GUI and assist in clustering the data.  Process the data in the GUI and use the clustering tab to generate these files.  The clustering tab allows tuning an epsilon parameter which controls how the clusters are separated, users should tune this parameter until good clusters are obtained, then in the merging phil identifiy the chosen cluster.  These covariance files and cluster numbers in the merging phils provide should be enough to reproduce this work.

You may wish to use multiprocessing, we recommend MPI:

mpirun -n X dials.stills_process mp.method=mpi ...
mpirun -n X cctbx.xfel.merge mp.method=mpi ...

Note, if merging using the deposited processing results instead of from scratch, the paths for the merging file are different, like this. For runs through 296:
input.path = processed/r0298/005_rg061/task197/combine_experiments_t005/intermediates/*reintegrated*
For runs 297-302:
input.path = processed/r0298/005_rg063/task197/combine_experiments_t005/intermediates/*reintegrated*

Please reach out to the authors with any questions.