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NaI-soaked lysozyme

This folder contains instructions and scripts for processing a lysozyme anomalous dataset. 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 differences.

We start with MTZ files found in ./unmerged_mtzs. These were processed by Precognition v5.2.2 (Renz Research, Inc.)

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 refinement script scripts/sbatch_phenix_Refine.sh, run using 2_HEWL_anom_refine.sh, requires sourcing your copy of phenix_env.sh, the environment script that comes with your copy of phenix.

After running careless, we postprocess the data and 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 where MTZ files from the Zenodo deposition belong. These files are too large to be added to github. unmerged_precognition.mtz contains unmerged intensities from 720 images of NaI-soaked lysozyme diffraction processed with Precognition (Renz Research, Inc.). *_{plus,minus}.mtz are the outputs of scripts/friedelize.py, which splits unmerged.mtz into F+ and F- half-datasets:
  python scripts/friedelize.py unmerged_mtzs/unmerged_precognition.mtz -p unmerged_mtzs/unmerged_precognition_plus.mtz -m unmerged_mtzs/unmerged_precognition_minus.mtz
  • 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.
  • careless_runs_pred: a folder containing a script for running careless as a batch array, used for calculating replicates of the CCpred statistic.
  • pymol: inputs to, and outputs from pymol for visualizing anomalous omit maps.
  • scripts: a folder containing various scripts that are used for postprocessing the output data. Included in scripts are:
    • 1_HEWL_anom_unfriedelize.sh: a script that converts output careless MTZ files into downstream readable files. This script relies on unfriedelize.py and unfriedelize_xval.py, two scripts that unsplit MTZ files that have been split into F+ and F- half-datasets by friedelize.py. This script is called in the main notebook, Inspect_Careless_param_grid.ipynb.
    • 2_HEWL_anom_refine.sh: a script that refines phases for the anomalous omit map. This script calls sbatch_phenix_Refine.sh, which relies on custom_refinement_param_*.eff and HEWL_starting_model*.pdb. This script is called in Inspect_Careless_param_grid.ipynb.
    • 3_HEWL_anom_peak_heights.sh: a script that computes anomalous omit peak heights from anomalous omit maps.
    • anomalous_peak_heights.py: a script called by run_ccs.sh that computes the anomalous peak heights at the iodine and sulfur anomalous scattering positions.
    • concatenate_anomalous_peak_csv.py: 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.
    • custom_refinement_param_*.eff: phenix .eff files used by 2_HEWL_anom_refine.sh for automated refinement of omit maps.
    • friedelize.py: a script used for splitting unmerged.mtz into anomalous half-datasets.
    • HEWL_starting_model*.pdb: starting model used by refinement in 3_HEWL_anom_peak_heights.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${\text{pred}}$, and CC$_\text{anom}$. This script is called in Inspect_Careless_param_grid.ipynb.
    • sbatch_phenix_Refine.sh: a script for calling phenix.refine.
    • 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.