PDBFixer fixes problems in PDB files
Python HTML Shell
Latest commit f040687 Feb 3, 2017 @peastman peastman committed on GitHub Merge pull request #148 from peastman/version
Updated version number to 1.4


Build Status


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