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Thermolysin

This folder contains instructions and scripts for analyzing anomalous signal from an XFEL dataset of thermolysin (CXIDB, entry 81; Dalton et al. 2022, Nat. Comm. 2022, https://doi.org/10.1038/s41467-022-35280-8). Here, we

  1. run careless with a bivariate prior, for many values of the double-Wilson r parameter, and then
  2. inspect merging statistics and anomalous difference peak heights.

We start with MTZ files found in ./unmerged_mtzs. These were converted from CXIDB entry 81.

To run careless, we use the script careless_runs/slurm-dw-array-grid.sh, which starts a slurm batch array job. This job requires careless_runs/slurm_params.txt, in which we vary the double-Wilson r value across the individual careless runs. To call using slurm:

cd careless_runs
sbatch slurm-dw-array-grid.sh

Many bash scripts require activating a conda environment with careless in it. Please take note that you are activating the right conda environment! Additionally, the two refinement scripts, scripts/launch_refinement.sh and scripts/launch_refinement_omit.sh, both require sourcing your copy of phenix_env.sh, the environment script that comes with your copy of phenix.

After running careless, we evaluate the quality of the careless results in the jupyter notebook titled Inspect_Careless_param_grid.ipynb. This notebook also plots figures.

Folders

  • unmerged_mtzs: a folder with three unmerged MTZ files. unmerged.mtz contains unmerged intensities from CXIDB entry 81. friedel_{plus,minus}.mtz are the outputs of scripts/friedelize.py, which splits unmerged.mtz into F+ and F- half-datasets.
  • careless_runs: a folder containing a script for running careless as a batch array, as well as the resultant subfolders containing outputs from individual runs of careless.
  • refinement: a folder containing reference pdb files as well as phenix .eff files for refinement of careless outputs. Additionally, the folder contains an MTZ file with reference R-free flags.
  • scripts: a folder containing scripts that are used for processing the output data. Included in scripts are:
    • anomalous_peak_heights.py: a script called by run_ccs.sh that computes the anomalous peak heights at the five anomalous scattering positions.
    • friedelize.py: the script used for splitting unmerged.mtz into F+ and F- half-datasets.
    • launch_refinement_omit.sh: a script for refining an omit model against careless outputs, where the model's anomalous scatterers have occupancy set to 0. This script is called in unfriedelize_all.sh.
    • launch_refinement.sh: a script for refining a model against against careless outputs. This script is called in unfriedelize_all.sh.
    • run_ccs.sh: a script for calculating CC$\text{1/2}$, CC${\text{pred}}$, CC$_\text{anom}$, and anomalous peak heights for each careless output. This script is called in Inspect_Careless_param_grid.ipynb.
    • unfriedelize_all.sh: A script that converts output careless MTZ files into downstream readable files. Additionally, this script starts refinement of the careless outputs. This script is called in Inspect_Careless_param_grid.ipynb.
    • unfriedelize.py: a script for unsplitting MTZ files that have been split by friedelize.py.