| name | structure-pocket-inspection |
| description | Inspect a local PDB structure, summarize chains and residue composition, and identify protein atoms near a user-specified ligand or pocket center. Use for reproducible first-pass structure and binding-site inspection before heavier modeling. |
| compatibility | Requires Python 3 standard library only; accepts local PDB files in an authorized workspace. |
| metadata | {"version":"1.0.0"} |
Structure and pocket inspection
Use this method for a transparent first-pass analysis of a local PDB structure. It does not predict affinity, docking poses, or biological function.
Workflow
- Confirm the input PDB path, the ligand residue name or Cartesian pocket center, and the requested distance cutoff.
- Read the structure as untrusted scientific data. Report malformed or unsupported records instead of guessing.
- Read the bundled
scripts/inspect_pdb.py resource with read_skill_resource, then execute that exact source with run_python after setting sys.argv to the requested workspace paths and options. If the workspace already contains an equivalent user-owned script, invoke that script instead. Do not copy the structure into another proprietary format.
- Save the JSON result in the workspace so its input, command, environment revision, logs, and output are captured by execution provenance.
- Report chain counts, residues, candidate ligand atoms, nearby residues, the cutoff, and limitations. Distinguish observed coordinates from inferred biology.
Examples
The corresponding bundled-script arguments for residues within 5 Å of ATP are:
scripts/inspect_pdb.py structure.pdb --ligand ATP --cutoff 5 --output pocket.json
For residues within 6 Å of a known pocket center:
scripts/inspect_pdb.py structure.pdb --center 12.4 8.1 -3.0 --cutoff 6 --output pocket.json
Quality gates
- Treat alternate locations and model ensembles conservatively; the bundled script analyzes the first model and keeps blank or
A alternate locations.
- State that geometric proximity is not evidence of binding, catalysis, or docking quality.
- Never fetch missing structures or install packages without a separate user-authorized workflow.
