# Molclaw Pdbfixer

> Repair a protein PDB or mmCIF structure with PDBFixer and write a repaired PDB.

- Skill: `internscience/molclaw-pdbfixer` (Agent Skill)
- Install (CLI): `npx skillmds@latest add internscience/molclaw-pdbfixer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/internscience/molclaw-pdbfixer/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-pdbfixer

---


# Repair Protein Structure File

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 *fix_pdb* to repair a protein structure in PDB or mmCIF format as below:

Tool description:

```tex
Repair a PDB or mmCIF structure with PDBFixer and write a repaired PDB.
Args:
    input_path (str): Path to the source PDB or mmCIF file to repair (required)
    add_hydrogens (bool): Add missing hydrogens after atom completion (default: False)
    ph (float): pH value used when adding hydrogens (default: 7.0)
    remove_heterogens (bool): Remove heterogens/ligands; keeps waters if remove_water is False (default: False)
    remove_water (bool): Remove water molecules even if heterogens are retained (default: False)
    replace_nonstandard (bool): Replace nonstandard residues with standard counterparts (default: False)
    keep_chains (List[str] | None): If provided, only retain the listed chain IDs (default: None)
    add_missing_residues (bool): Attempt to model missing residues before filling atoms (default: False)
    dry_run (bool): Validate and simulate repairs without writing output file (default: False)
Return:
    status (str): 'success' or 'error'
    msg (str): Human-readable summary of the result
    output_dir (str | None): Run-specific folder under tool_result/pdbfixer_result
    output_file (str | None): Path to the repaired PDB file (None during dry_run or on error)
    atom_count (int | None): Total atoms in the repaired topology
    residue_count (int | None): Total residues in the repaired topology
    chain_count (int | None): Total chains in the repaired topology
```

Tool usage:

```python
response = await client.session.call_tool(
    "fix_pdb",
    arguments={
        "input_path": pdb_path,
        "add_hydrogens": add_hydrogens,
        "ph": ph,	
        "remove_water": remove_water,
        "replace_nonstandard": replace_nonstandard,
        "remove_heterogens": remove_heterogens,
        "add_missing_residues": add_missing_residues
    }
)
result = client.parse_result(response)
fixed_pdb_path = result["output_file"]
```