https://github.com/joseph-ellaway/per-residue-distance
Calculates the per-residue atomic distance between two proteins
https://github.com/joseph-ellaway/per-residue-distance
bioinformatics bioinformatics-tool euclidean-distances gemmi matplotlib pdbe protein-structure rmsd structural-biology
Last synced: about 2 months ago
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Calculates the per-residue atomic distance between two proteins
- Host: GitHub
- URL: https://github.com/joseph-ellaway/per-residue-distance
- Owner: Joseph-Ellaway
- License: mit
- Created: 2024-01-05T15:35:25.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-01-05T15:38:20.000Z (over 1 year ago)
- Last Synced: 2025-02-12T01:54:32.768Z (3 months ago)
- Topics: bioinformatics, bioinformatics-tool, euclidean-distances, gemmi, matplotlib, pdbe, protein-structure, rmsd, structural-biology
- Language: Python
- Homepage:
- Size: 326 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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/[0]//.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/_updated.cif```
E.g.
```wget https://www.ebi.ac.uk/pdbe/entry-files/download/7cyr_updated.cif```
## Example
``` python
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.