molclaw-fix-pdb

You can repair a PDB file by using PDBFixer to add missing hydrogens, model absent residues, and remove heterogens or waters, producing a cleaned structure ready for simulation.

Structure cleaning fixes incomplete protein structures by modeling missing residues and removing unwanted heterogens or waters. This ensures the protein structure has a complete topology and valid geometry for downstream docking or simulation tasks.

Yes, you can add hydrogens and remove heterogens from a PDB simultaneously. The repair process applies parameterized control over structure cleaning options, allowing you to handle both tasks and produce a complete, valid topology.

To verify topology counts after fixing a protein structure, the repair process outputs simple topology counts including atoms, residues, and chains. These counts are generated alongside the repaired PDB file for validation and reproducibility.

You should use PDBFixer for structure preparation when you have broken or incomplete PDB structures that need hydrogens, missing residue modeling, or heterogen removal before running molecular dynamics simulations or docking workflows.

Yes, PDB repair includes validation before writing results. The process checks the repaired structure and saves the final output file and topology counts to run-specific directories to ensure reproducibility.