Structure cleanup
Fills in missing residues and atoms, replaces nonstandard residues, adds hydrogens at a chosen pH, and optionally strips waters/ligands, via PDBFixer. Use to prep a structure before docking or simulation, especially one pulled straight from a crystal structure.
Structure cleanup
What it does
Takes one structure and runs it through the standard prep pass most structural work needs before it's actually usable — a crystal structure almost never comes out of the PDB complete, since disordered regions, unresolved side chains, and hydrogens (which X-ray rarely resolves at all) are the normal state of things, not the exception.
In one run:
- Missing residues are found (gaps in the chain)
- Nonstandard residues are replaced with their standard equivalents (a modified amino acid becomes the parent one it's based on)
- Missing atoms — an incomplete side chain, a missing backbone oxygen — are added
- Hydrogens are added, at whatever pH is set (default 7.0, physiological)
- Heterogens — waters, bound ligands, ions — are optionally stripped
Choosing what to remove
Three choices control heterogens:
- Keep everything (default) — nothing is removed, only added
- Remove heterogens, keep water — ligands and ions go, ordered waters stay
- Remove all heterogens, including water — a bare protein/nucleic acid, nothing else
Removing everything is the usual prep before docking a new ligand in — existing waters and any co-crystallized ligand would otherwise occupy the site being docked into.
Reading the output
The summary reports what was actually found and changed: how many residues were missing, how many were nonstandard and replaced, how many atoms were added, how many hydrogens were added, how many heterogen residues were removed. A structure that was already complete will show zeros across the board — that's a real answer, not a sign anything went wrong.
Input
One structure, saved as a PDB or mmCIF file.
Important limitations
Added atoms get reasonable starting positions, not a minimized structure. PDBFixer places missing atoms using standard geometry templates; it doesn't run any kind of energy minimization. If a relaxed structure is needed, that's a job for a molecular dynamics step afterward.
The output is always PDB, regardless of what format was given. Use Format conversion afterward if a different format is needed.
Missing residues are filled with standard geometry, not the true structure. A large gap gets a plausible but generic backbone — real electron density for that region simply doesn't exist, and no tool can recover it.