PDBFixer fixes problems in PDB files
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peastman Merge pull request #177 from JoaoRodrigues/reproducible_addatoms
Added a seed parameter to addMissingAtoms to allow reproducible results
Latest commit 4cea9a7 Oct 5, 2018


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PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems:

  • Add missing heavy atoms.
  • Add missing hydrogen atoms.
  • Build missing loops.
  • Convert non-standard residues to their standard equivalents.
  • Select a single position for atoms with multiple alternate positions listed.
  • Delete unwanted chains from the model.
  • Delete unwanted heterogens.
  • Build a water box for explicit solvent simulations.

See our manual