A protein structure can look perfectly reasonable in a viewer and still contain details that complicate docking or simulation: alternate atom positions, missing atoms, extra solvent, or clashes. The tricky part is that “cleaning” and “repairing” are not the same task. Removing unnecessary contents may be enough for one workflow; a structure with missing residues needs a more substantial fix.
A useful approach is to prepare the structure in stages: first decide what should remain, then apply routine cleanup, and finally check whether anything needs repair. This helps avoid treating every structure the same way—and makes it easier to understand what changed before moving on to downstream calculations.
1. Decide what belongs in your model
Before deleting anything, consider the purpose of the model. A ligand, cofactor, ion, or water molecule may be unnecessary for a particular workflow, but some may be relevant to the system you want to study. SAMSON’s preparation tools can remove ligands (including covalently attached ligands), water, and monatomic ions, so review what is present and choose the cleanup options deliberately.
Alternate locations are another common source of ambiguity. A PDB structure may include multiple positions for an atom. SAMSON can keep the highest-occupancy position; when occupancies are tied or absent, it uses the available alternate-location labels according to its selection rule. If you want to inspect the choices before changing the structure, use Home > Validate, open the Alt. locations tab, and select Find alternate locations.
2. Use quick preparation for routine cleanup
For a structure that is otherwise in good shape, Home > Prepare applies common preparation steps in one place. Depending on the selected options, it can remove alternate locations, delete unwanted ligands, strip water, clear monatomic ions, and add hydrogens.
Hydrogens are added by residue type for standard residues or by valence. SAMSON’s standard hydrogen addition is based on pH 7 for standard amino and nucleic acid residues; it uses valences for other structures. That is a convenient starting point, but it is not a substitute for checking whether a workflow needs a different protonation treatment.
If you are preparing many structures, the Batch Protein Prepare extension can process files in a folder or download structures using PDB identifiers, then apply the same cleaning steps. This is useful when you need consistent preparation across a set rather than repeating the same actions manually.
3. Validate before assuming the structure is ready
Cleanup does not automatically resolve every structural problem. In Home > Validate, you can inspect alternate locations, bond lengths outside expected ranges, non-standard residue naming, and clashes or contacts. Validation is particularly useful as a checkpoint: it helps distinguish a structure that only needed routine cleanup from one that requires targeted attention.
For example, if side chains clash, the Rotamers editor can be used to change side-chain conformations based on a backbone-dependent rotamer library. Validation also includes tools to merge nodes, reorder atoms in a connected component, and renumber atom serial numbers—details that can matter when preparing tidy atom and node lists for simulations.
4. Switch to deeper repair when atoms or residues are missing
If the structure has missing residues or atoms, routine cleanup is not enough. The PDBFixer extension 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 resolve alternate locations, remove water or heterogens, and build explicit-solvent water boxes or lipid membranes around membrane proteins.
That distinction is worth keeping in mind: use the quick preparation step for common cleanup, and turn to PDBFixer when the model itself has gaps or missing atoms that need to be built. After either path, check the resulting structure against the needs of your docking, simulation, or analysis workflow.
For step-by-step instructions and additional details, read the protein preparation and validation tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.