This extension integrates the PDBFixer Python package and exposes its functionality.

PDBFixer fixes issues in Protein Data Bank (PDB) files (supported formats: PDB, mmCIF/PDBx) in preparation for simulating them. It can 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 heterogens.
• Build a water box for explicit solvent simulations.
• Build a membrane around a protein.

Tutorial

See: Protein Preparation & Validation: Fixing Deeper Problems with PDBFixer.

References

[1] PDBFixer Python package. https://github.com/openmm/pdbfixer

[2] Eastman P. et al. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659