# Molclaw Extract Chains

> Extract protein sequence of each chain from the protein structure file (pdb format).

- Skill: `internscience/molclaw-extract-chains` (Agent Skill)
- Install (CLI): `npx skillmds@latest add internscience/molclaw-extract-chains`
- Raw SKILL.md: https://api.skillmd.com/api/skills/internscience/molclaw-extract-chains/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: MIT license
- Author: internscience (https://skillmd.com/u/internscience)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/internscience/molclaw-extract-chains

---


# Extract Protein Chains

Note: 
- Local files are not directly accessible by the server. Please upload them to the server using `molclaw-file-transfer` before execution. 
- For PDB file inputs, it is recommended to preprocess them using `molclaw-pdbfixer` before execution.
- Please refer to skill `molclaw-scp-server` to complete tool invocation.

Use tool *extract_pdb_chains* to extract protein chains from the repaired pdb file

Tool description:

```tex
Extract the amino acid sequence of each chain from the PDB file.
Args:
    pdb_file_path (str): Path to input pdb file
Return:
    status (str): success/error
    msg (str): message
    chains (List[dict]): List of dict, each containing the keys 'chain' and 'sequence'.
        --chain (str): Chain ID
        --sequence (str): Sequence string
```

Tool usage:

```python
response = await client.session.call_tool(
    "extract_pdb_chains",
    arguments={
        "pdb_file_path": fixed_pdb_path
    }
)
result = client.parse_result(response)
protein_chains = result['chains']
```