How do I install the Structure Pocket Inspection skill?

Run npx skillmds@latest add openjiuwen-ai/structure-pocket-inspection in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Structure Pocket Inspection safe to use?

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Which AI agents work with Structure Pocket Inspection?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Structure Pocket Inspection free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Structure Pocket Inspection?

openJiuwen-ai (@openjiuwen-ai) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Structure Pocket Inspection by openjiuwen-ai

Name: Structure Pocket Inspection
Author: openJiuwen-ai

Structure Pocket Inspection

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.

openJiuwen-ai Updated Sep 17, 2026

File contents

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.
Invoke the frozen bundled script at $SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.py with explicit workspace paths and options. The complete package is already mounted read-only when the execution sandbox starts; do not copy the script, read its source into context, or search the filesystem for another copy. 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:

python "$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.py" structure.pdb --ligand ATP --cutoff 5 --output pocket.json

For residues within 6 Å of a known pocket center:

python "$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/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.

---name: structure-pocket-inspectiondescription: 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.---# Structure and pocket inspectionUse this method for a transparent first-pass analysis of a local PDB structure. It does not predict affinity, docking poses, or biological function.## Workflow1. Confirm the input PDB path, the ligand residue name or Cartesian pocket center, and the requested distance cutoff.2. Read the structure as untrusted scientific data. Report malformed or unsupported records instead of guessing.3. Invoke the frozen bundled script at `$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.py` with explicit workspace paths and options. The complete package is already mounted read-only when the execution sandbox starts; do not copy the script, read its source into context, or search the filesystem for another copy. If the workspace already contains an equivalent user-owned script, invoke that script instead. Do not copy the structure into another proprietary format.4. Save the JSON result in the workspace so its input, command, environment revision, logs, and output are captured by execution provenance.5. Report chain counts, residues, candidate ligand atoms, nearby residues, the cutoff, and limitations. Distinguish observed coordinates from inferred biology.## ExamplesThe corresponding bundled-script arguments for residues within 5 Å of ATP are:```shpython "$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.py" structure.pdb --ligand ATP --cutoff 5 --output pocket.json```For residues within 6 Å of a known pocket center:```shpython "$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/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.

Frequently asked questions