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Inspect a local PDB structure, summarize chains and residue composition, and identify protein atoms near a user-specified ligand or pocket center.
Apache-2.0Auto-check passed
Install Structure Pocket Inspection
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspection --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/structure-pocket-inspection .claude/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .claude/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspectionType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspection --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/structure-pocket-inspection .agents/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .agents/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspection --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/structure-pocket-inspection .cursor/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .cursor/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/openJiuwen-ai/sciencediscovery.git --path skills/structure-pocket-inspection--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspection --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/structure-pocket-inspection .gemini/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .gemini/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspectionInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/structure-pocket-inspection .github/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .github/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install openJiuwen-ai/sciencediscovery structure-pocket-inspection --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/openJiuwen-ai/sciencediscovery.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/structure-pocket-inspection .opencode/skills/structure-pocket-inspection && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "structure-pocket-inspection" agent skill from https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection into .opencode/skills/structure-pocket-inspection/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-pocket-inspection", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
structure-pocket-inspection- GitHub stars
- 162
- Token cost
- ~624 tokens
- SKILL.md length
- 241 words
- Files
- 2 (incl. scripts)
- Skills in repo
- 23
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Inspect a local PDB structure, summarize chains and residue composition, and identify protein atoms near a user-specified ligand or pocket center.
- Works in 5 steps: Confirm the input PDB path, the ligand… → Read the structure as untrusted… → Invoke the frozen bundled script at… → …
- Reproducible first-pass structure and binding-site inspection before heavier modeling
- SKILL.md covers Workflow, Examples and Quality gates
- Runs Python scripts from its folder; calls python
What it does
Structure Pocket Inspection is an agent skill from openJiuwen-ai/sciencediscovery. 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.
Its SKILL.md is about 620 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including scripts (for example `scripts/inspect_pdb.py`). Compatibility notes: Requires Python 3 standard library only; accepts local PDB files in an authorized workspace.
The repository describes itself as: ScienceDiscovery is an all‑in‑one agentic workbench built specifically for scientific research. The licence is Apache-2.0.
When your agent uses it
- Reproducible first-pass structure and binding-site inspection before heavier modeling
Example prompts
- “/structure-pocket-inspection”
Requirements
- Python 3
- Compatibility (from SKILL.md): Requires Python 3 standard library only; accepts local PDB files in an authorized workspace.
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- 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…
- 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…
What it can do on your machine
Read from SKILL.md and the folder at commit cc95884. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Compatibility
Requires Python 3 standard library only; accepts local PDB files in an authorized workspace.
From compatibility in the SKILL.md frontmatter.
Context cost
Structure Pocket Inspection loads about 624 tokens when it runs. Until then it costs about 67 tokens; SKILL.md has 241 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from openJiuwen-ai/sciencediscovery at commit cc95884, republished under its Apache-2.0 licence (© openJiuwen-ai). 241 words, ~624 tokens.
Download SKILL.mdSave it as
.claude/skills/structure-pocket-inspection/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- 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.
- Invoke the frozen bundled script at
$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.pywith explicit workspace paths and options. The complete package is already mounted read-only when the execution sandbox starts; do not copy the script, read its source into context, or search the filesystem for another copy. If the workspace already contains an equivalent user-owned script, invoke that script instead. Do not copy the structure into another proprietary format. - Save the JSON result in the workspace so its input, command, environment revision, logs, and output are captured by execution provenance.
- Report chain counts, residues, candidate ligand atoms, nearby residues, the cutoff, and limitations. Distinguish observed coordinates from inferred biology.
Examples
The corresponding bundled-script arguments for residues within 5 Å of ATP are:
python "$SCIENCEDISCOVERY_SKILLS_DIR/structure-pocket-inspection/scripts/inspect_pdb.py" structure.pdb --ligand ATP --cutoff 5 --output pocket.jsonFor 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.jsonQuality gates
- Treat alternate locations and model ensembles conservatively; the bundled script analyzes the first model and keeps blank or
Aalternate 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.
© openJiuwen-ai, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file (scripts) in skills/structure-pocket-inspection of openJiuwen-ai/sciencediscovery.
- SKILL.md
- scripts/inspect_pdb.py
Open the folder on GitHubat commit cc95884
Compare with similar skills
Structure Pocket Inspection next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Structure Pocket Inspection this skillopenJiuwen-ai/sciencediscovery | 162 | — | ~624 | Automated safety check: Pass | Apache-2.0 | |
| Summarizeopenclaw/openclaw | 392k | 1 repos | ~531 | Automated safety check: Pass | MIT | |
| Research Summarizeralirezarezvani/claude-skills | 28k | 1 repos | ~2.7k | Automated safety check: Pass | MIT | |
| Node Inspect Debuggeropenclaw/openclaw | 392k | 1 repos | ~894 | Automated safety check: Pass | MIT | |
| Sbom Supply Chainsickn33/agentic-awesome-skills | 47k | 2 repos | ~3.4k | Automated safety check: Pass | MIT | |
| Agent Supply Chaingithub/awesome-copilot | 40k | 1 repos | ~2.7k | Automated safety check: Pass | MIT |
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Questions about Structure Pocket Inspection
What does Structure Pocket Inspection do?
Inspect a local PDB structure, summarize chains and residue composition, and identify protein atoms near a user-specified ligand or pocket center. Structure Pocket Inspection is an agent skill from openJiuwen-ai/sciencediscovery. Inspect a local PDB structure, summarize chains and residue composition, and identify protein atoms near a user-specified ligand or pocket center.
When should I use Structure Pocket Inspection?
Structure Pocket Inspection fits situations like: reproducible first-pass structure and binding-site inspection before heavier modeling.
How do I install Structure Pocket Inspection in Claude Code?
Run `npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a claude-code`. Or copy the skill folder (skills/structure-pocket-inspection in openJiuwen-ai/sciencediscovery) into .claude/skills/structure-pocket-inspection in your project. Claude Code loads it when a task matches its description.
How do I install Structure Pocket Inspection in Codex?
Run `npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a codex`. Or copy the skill folder (skills/structure-pocket-inspection in openJiuwen-ai/sciencediscovery) into .agents/skills/structure-pocket-inspection in your project. Codex loads it when a task matches its description.
Can I use Structure Pocket Inspection in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/structure-pocket-inspection, .gemini/skills/structure-pocket-inspection, .github/skills/structure-pocket-inspection and .opencode/skills/structure-pocket-inspection in your project.
What does Structure Pocket Inspection need to run?
Going by SKILL.md and its folder, Structure Pocket Inspection needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3. Compatibility (from SKILL.md): Requires Python 3 standard library only; accepts local PDB files in an authorized workspace..
Does Structure Pocket Inspection access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Structure Pocket Inspection safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Structure Pocket Inspection use?
Structure Pocket Inspection is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Structure Pocket Inspection use?
About 624 tokens (SKILL.md is roughly 2.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Structure Pocket Inspection?
Skills that share tags, products or a category with Structure Pocket Inspection: Summarize (openclaw/openclaw, 392k stars), Research Summarizer (alirezarezvani/claude-skills, 28k stars), Node Inspect Debugger (openclaw/openclaw, 392k stars) and Sbom Supply Chain (sickn33/agentic-awesome-skills, 47k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Structure Pocket Inspection?
openJiuwen-ai (a GitHub organization) maintains it in openJiuwen-ai/sciencediscovery, which has 162 GitHub stars. The repository holds 23 skills in this directory. The repository was last updated on October 11, 2026.
Source: openJiuwen-ai/sciencediscovery on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.