Attention it is just a fork to be able to pip install it

Good

PDBFixer

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

Installation

PDBFixer can be installed with conda or mamba.

conda install -c conda-forge pdbfixer

Alternatively you can install from source, as described in the manual.