covid-moonshot-manuscript

Scripts, figures, and data relevant to the COVID moonshot manuscript.

Organisation

scripts: contains PyMol and Python scripts used to create protein - ligand images. In order to run these scripts the aligned structures and metadata.csv are required. These can be downloaded via:

wget https://fragalysis.diamond.ac.uk/media/targets/Mpro.zip

It is recommened that the .zip file is extracted in the ./data directory of this repository since that is where all scripts in the ./figures README.md files are referenced to.

Mpro data structure

• Run unzip MPro.zip to extract the relevant files.
• The aligned/ directory contains all aligned MPro structures.
• metadata.csv contains relevant information for fragment names etc.

Examples

• Check the README.md appropriate files in the ./figures directory for example terminal commands used to create each figure.
• A working installation of PyMol is required.
• It is also recommended to have the following line in your ./pymolrc to access colour blind friendly colours:

run https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/colorblindfriendly.py