dw-examples

Examples of merging crystallographic intensities with a bivariate prior

Setup

To run much of the scripts and notebooks in this repository, Careless and rs-booster must be installed. Many scripts activate a conda environment with Careless installed, e.g.:

run_ccs.sh

#please indicate your desired careless environment here!
eval "$(conda shell.bash hook)"
conda activate careless

Please change the name of the conda environment as needed.

Additionally, some scripts require sourcing Phenix, e.g.: run_ccs.sh

# source your copy of phenix here!
source /n/holylfs05/LABS/hekstra_lab/Lab/garden/phenix/phenix-1.20.1-4487/phenix_env.sh

Please change the path of the phenix environment file as needed.

Finally, all jobs were run on a computing cluster, so certain Careless scripts require slurm to run.

Examples

For every example, there is a README.md that describes the contents of each example folder. Additionally, every example includes scripts to run careless as well as to analyze the outputs in order to reproduce the figures in the double-Wilson manuscript. The examples are:

• time-resolved Laue crystallography of the photoactive yellow protein
• anomalous diffraction from serial XFEL crystallography of thermolysin
• anomalous diffraction from Laue crystallography of NaI-soaked lysozyme
• fragment screening monochromatic data of Nsp3 Mac1