A docking setup can look ready while the structure still contains alternate atom positions, unwanted waters, or missing atoms. These details are easy to overlook when you are eager to get to the modeling—but they can create avoidable problems later. A useful first step is to decide whether your protein needs routine cleanup or a deeper structural repair.
SAMSON offers both paths. Home > Prepare is a convenient starting point for common cleanup. The Structure Validation tools help you inspect specific issues, while the PDBFixer extension addresses problems such as missing residues and atoms. The key is to choose cleanup steps with your downstream task in mind: a molecule that is unnecessary for one workflow may be important to another.
Start with the questions that affect your workflow
Before removing anything, consider what the model is for. Are you preparing a protein for docking, simulation, or structure analysis? Do you need a bound ligand, cofactor, ion, or water molecule to remain? Is the structure already complete, or are residues or atoms missing? These checks help prevent a common preparation mistake: treating every non-protein component as disposable, even when it matters to the system you want to study.
If the structure appears clean and complete, the one-click preparation step may be sufficient. If it has missing residues, missing atoms, or protonation needs that require a chosen pH, use the deeper-fix options instead.
Use one-click preparation for routine cleanup
In SAMSON, choose Home > Prepare to run several common steps together. The tool can resolve alternate locations by keeping the highest-occupancy atoms, delete selected ligands and other small molecules, strip water, clear monatomic ions, and add hydrogens.
Alternate locations deserve particular attention. In a structure file, an atom may have more than one recorded position. The preparation step keeps the higher-occupancy position; when occupancies are equal or absent, it applies a preference for location A when available, then B, and so on. This gives you a consistent structure, but it is still worth considering whether the choice suits your analysis.
Be deliberate with deletion options. Removing water, ions, ligands, or cofactors can simplify a model, but those components may be relevant to a particular binding site or experiment. Review what will be removed rather than assuming that every small molecule is irrelevant.
When the structure needs more than cleanup
Routine preparation is not the same as rebuilding missing parts. If residues or atoms are absent, the PDBFixer extension can help. Depending on the structure and your choices, it can add missing residues based on SEQRES records, add missing heavy atoms and side chains, convert non-standard residues to standard equivalents, and add hydrogens for a specified pH. It can also process files in batches.
PDBFixer includes options for building explicit-solvent water boxes and lipid membranes. Those options are relevant when preparing a system for workflows that need them; they are not a substitute for deciding what biological components your model should contain.
Validate the result, not just the input
After cleanup or repair, open Home > Validate to inspect the structure. You can find alternate locations, check bonds outside expected length ranges, inspect non-standard residue names, and highlight clashes and contacts. If side-chain clashes need correction, the documentation points to the Rotamers editor as an option for changing side chains using a backbone-dependent rotamer library.
Validation also includes tools for keeping atom and node lists orderly, such as merging nodes, reordering atoms in a connected component, and renumbering atom serial numbers. These checks are especially useful before handing a structure to another tool or workflow, where problems can be harder to trace back to their source.
A short decision path
- Inspect what is present. Identify components you may need to preserve and look for missing residues or atoms.
- Choose the right level of work. Use Home > Prepare for common cleanup; use PDBFixer when the structure needs rebuilding or pH-specific hydrogens.
- Review the result. Run validation checks and address issues relevant to your downstream workflow.
One final detail: adding hydrogens does not automatically mean you must minimize the whole system. The right choice depends on the task. For example, the documentation notes that AutoDock Vina needs only polar hydrogens for determining hydrogen bonds.
For the complete workflow and further details, read the protein preparation and validation tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.