README.md

Plotting code for per-residue atomic distances

Obtain rotation-translation matrices from the PDBe FTP server:

https://ftp.ebi.ac.uk/pub/databases/pdbe-kb/superposition/<uniprot>[0]/<uniprot>/<uniprot>.json

E.g.

wget https://ftp.ebi.ac.uk/pub/databases/pdbe-kb/superposition/A/A0QTT2/A0QTT2.json

Obtain updated mmCIF files (the normal, non-SIFTS mmCIF file type will not work) using:

https://www.ebi.ac.uk/pdbe/entry-files/download/<pdbid>_updated.cif

E.g.

wget https://www.ebi.ac.uk/pdbe/entry-files/download/7cyr_updated.cif

Example

python3 per_residue_distance.py --mmcif1 example_data/7cyr_updated.cif.gz --mmcif2 example_data/7cy2_updated.cif.gz --rt_matrices example_data/A0QTT2.json --pdb_id1 7cyr --pdb_id2 7cy2 --chain1 A --chain2 A

Chain IDs should be parsed as label_asym_id from the updated mmcif atom_site loop.