The data for this paper were processed from experiments mfxlv4318 and mfxlu5017 using the cctbx.xfel GUI:
Brewster AS, Young ID, Lyubimov A, Bhowmick A, Sauter NK (2019): Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI. Computational Crystallography Newsletter 10, 22-39.

https://cci.lbl.gov/publications/download/CCN_2019_p22_Brewster.pdf

Folders:
$WORKING: this is where the data from this deposition has been unpacked.  Expand this in the below instructions.
$EXPT: this is either $WORKING/mfx/mfxlv4318  or $WORKING/mfx/mfxlu5017. Expand this in the below instructions.
xtc: xtc streams
geom: contains refined geometry file for the Rayonix detector
masks: trusted pixel masks for the Rayonix detector

Install the GUI using these instructions:
https://github.com/cctbx/cctbx_project/tree/master/xfel/conda_envs#general-build

Configure using these instructions:
https://github.com/cctbx/cctbx_project/tree/master/xfel/conda_envs#lcls-environment

Test the configuration with

$ detnames exp=mfxlu5017:run=165

You should get this output:
---------------------------------------------------
Full Name                  | DAQ Alias | User Alias
---------------------------------------------------
MfxEndstation.0:Epix100a.1 | ePix100_2 |
MfxEndstation.0:Epix100a.0 | ePix100_1 |
EBeam                      |           |
PhaseCavity                |           |
FEEGasDetEnergy            |           |
FEE-SPEC0                  |           |
MFX-DG1-BMMON              |           |
MFX-DG2-BMMON              |           |
NoDetector.0:Evr.0         | evr0      |
MfxEndstation.0:Rayonix.0  | Rayonix   |
ControlData                |           |
---------------------------------------------------

Experiment mfxlu5017
Runs tab: watch for new runs and tag runs 165-168 with cyp121

Trials tab: create a new trial with these parameters:

dispatch {
  integrate = False
  hit_finder {
    minimum_number_of_reflections = 40
  }
}
spotfinder {
  filter {
    min_spot_size = 2
  }
  threshold {
    dispersion {
      gain = 0.46
      global_threshold = 100
    }
  }
}
indexing {
  known_symmetry {
    space_group = "P 65 2 2"
    unit_cell = 77.184 77.184 263.83 90 90 120
  }
  refinement_protocol {
    d_min_start = 2
  }
  multiple_lattice_search {
    max_lattices = 3
  }
}

Create a new rungroup for runs 165-168. Extra phil parameters:
input.reference_geometry = $EXPT/geom/split_0000.expt

Then fill in the rest of the rungroup parameters:
Start run: 165, End run: 168
Beam X/Y/Detz: 960, 960, 194.02
Detector: MfxEndstation.0:Rayonix.0
binning: 4
Untrusted Pixel Mask: $EXPT/masks/pixels.mask

Mark the trial as active and Auto-submit jobs

Dataset tab:
Create a new dataset, using the cyp121 tag, named cyp121_lu50_1.65.
Add these tasks:
indexing: (no params)
ensemble_refinement:
combine_experiments.clustering.use=False
reintegration {
  integration {
    absorption_correction {
      apply = True
      algorithm = fuller_kapton *kapton_2019 other
      fuller_kapton {
        xtal_height_above_kapton_mm {
          value = 0.04
        }
        rotation_angle_deg {
          value = 0.55
        }
        kapton_half_width_mm {
          value = 0.53
        }
        kapton_thickness_mm {
          value = 0.025
        }
        smart_sigmas = True
      }
    }
    debug {
      output = True
      separate_files = False
    }
    summation {
      detector_gain = 0.46
    }
  }
}

scaling:
dispatch.step_list=input balance model_scaling modify filter errors_premerge scale postrefine statistics_unitcell statistics_beam model_statistics statistics_resolution
input.parallel_file_load.method=uniform
filter.outlier.min_corr=-1
filter.algorithm=unit_cell
filter.unit_cell.value.relative_length_tolerance=0.03
select.algorithm=significance_filter
select.significance_filter.sigma=0.1
select.significance_filter.min_ct=200
select.significance_filter.max_ct=300
scaling.model=$WORKING/5wp2_CYP121.pdb
scaling.resolution_scalar=0.96
merging.d_min=1.65
merging.merge_anomalous=True
postrefinement.enable=True
statistics.n_bins=20
output.do_timing=True
output.save_experiments_and_reflections=True

merging:
dispatch.step_list=input model_scaling statistics_unitcell statistics_beam model_statistics statistics_resolution group errors_merge statistics_intensity merge statistics_intensity_cxi
input.parallel_file_load.method=uniform
scaling.model=$WORKING/5wp2_CYP121.pdb
scaling.resolution_scalar=0.96
statistics.n_bins=20
merging.d_min=1.65
merging.merge_anomalous=True
merging.error.model=ev11
output.do_timing=True

Experiment mfxlv4318
NOTE NOTE NOTE: mfxlv4318 was processed without time-dependent ensemble refinement (see Brewster 2018).  It is advised if reprocessing these data to use parameters more similar to mfxlu5017.

Runs tab: watch for new runs and tag runs 193-196 and runs 198-200 with Cyp_200ms

Trials tab: create a new trial with these parameters:

dispatch {
  hit_finder {
    minimum_number_of_reflections = 10
  }
}
spotfinder {
  filter {
    min_spot_size = 2
  }
}
indexing {
  known_symmetry {
    space_group = "P 65 2 2"
    unit_cell = 78.61 78.61 265.98 90 90 120
  }
  multiple_lattice_search {
    max_lattices = 3
  }
  stills {
    method_list = fft1d real_space_grid_search
  }
}
integration {
  debug {
    output = True
    separate_files = False
  }
  absorption_correction {
    apply = True
    algorithm = fuller_kapton *kapton_2019 other
    fuller_kapton {
      xtal_height_above_kapton_mm {
        value = 0.005
      }
      rotation_angle_deg {
        value = 226.5
      }
      kapton_half_width_mm {
        value = 0.79
      }
      kapton_thickness_mm {
        value = 0.025
      }
      smart_sigmas = True
    }
  }
}

Create three rungroups: 1) runs 193-193, 2) runs 194-194, 3) runs 195-200.
Extra phil parameters for rungroups 1 and 3:
input.reference_geometry = $EXPT/geom/172.expt
For rungroup 2:
input.reference_geometry = $EXPT/geom/384.expt

Then fill in the rest of the rungroup parameters:
Beam X/Y/Detz: 960, 960, 580 (note the 580 is a placeholder, the real distance is in the .expt file)
Detector: MfxEndstation.0:Rayonix.0
binning: 4
spectrum_eV_per_pixel=0.043
spectrum_eV_offset=9479.3
Untrusted Pixel Mask for rungroups 1 and 3: $EXPT/masks/polypico_172_2.mask
For rungroup 2: $EXPT/masks/384_2.mask

Mark the trial as active and Auto-submit jobs

Dataset tab:
Create a new dataset, using the Cyp_200ms tag, named Cyp_1.85A_200ms_MD.
Add these tasks:
indexing: (no params)
scaling:
dispatch.step_list=input balance model_scaling modify filter errors_premerge scale postrefine statistics_unitcell statistics_beam model_statistics statistics_resolution
input.parallel_file_load.method=uniform
filter.outlier.min_corr=-1
filter.algorithm=unit_cell
select.algorithm=significance_filter
select.significance_filter.sigma=0.1
scaling.model=$WORKING/5wp2.pdb
scaling.resolution_scalar=0.95
scaling.mtz.mtz_column_F=Iobs
merging.d_min=1.8
merging.merge_anomalous=True
postrefinement.enable=True
output.do_timing=True
output.save_experiments_and_reflections=True

merging:
dispatch.step_list=input model_scaling statistics_unitcell statistics_beam model_statistics statistics_resolution group errors_merge statistics_intensity merge statistics_intensity_cxi
input.parallel_file_load.method=uniform
scaling.model=$WORKING/5wp2.pdb
scaling.resolution_scalar=0.95
statistics.n_bins=20
merging.d_min=1.85
merging.merge_anomalous=True
merging.error.model=ev11
output.do_timing=True