molclaw-pdbfixer

What problem does it solve?

This Skill automates repair and standardization of protein PDB structure files to fix missing atoms and residues, add hydrogens at a specified pH, remove heterogens or waters, and replace nonstandard residues to produce validated files for downstream modeling.

Core Features & Use Cases

• PDB repair and completion: Fill missing atoms and optionally model missing residues before atom completion.
• Chemical cleaning: Add hydrogens with pH control, remove heterogens or water molecules, and replace nonstandard residues.
• Validation and outputs: Reports atom, residue, and chain counts and writes a repaired PDB file; supports dry-run validation without writing files.
• Use Case: Prepare experimental structures for docking, virtual screening, or molecular dynamics by ensuring complete and standardized topology.

Quick Start

Use molclaw-pdbfixer to repair 'input.pdb', add hydrogens at pH 7.0, remove heterogens, and download the repaired PDB to the local workspace.