PDBFixer fixes problems in PDB files
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peastman Merge pull request #168 from peastman/single
Fixed error when a file contains only one residue
Latest commit 6c1caa9 May 23, 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