A protein structure can look perfectly reasonable on screen and still be a poor starting point for docking or simulation. Alternate atom positions, missing atoms, unresolved loops, or unsuitable protonation can all complicate downstream work. The key is to distinguish routine cleanup from structural repair: removing unwanted molecules is not the same as rebuilding missing parts.
A practical first question is: what is actually wrong with this model? The answer determines whether a quick preparation is enough or whether you need a more targeted repair.
Start with the quick cleanup—carefully
In SAMSON, Home > Prepare applies several common cleanup steps together. It can keep one position for atoms with alternate locations, delete selected ligands and other small molecules, strip waters, clear monatomic ions, and add hydrogens.
For alternate locations, the tool retains the highest-occupancy atoms. When occupancies are tied or absent, it uses the available alternate-location labels in a defined order, preferring A when present. This helps produce a single-coordinate model, but it is still worth checking that the retained positions make sense for the structure you intend to study.
Be deliberate about deleting molecules. A ligand, cofactor, ion, or water may be unnecessary for one workflow but important for another. In particular, if the molecule is part of the biological system you are modeling, remove it only when that matches your scientific question.
Inspect before you assume the structure is ready
Use Home > Validate to check for issues that a one-click cleanup does not resolve. The Structure Validation module can find alternate locations, flag bonds outside expected length ranges, identify non-standard residue aliases, and highlight clashes or contacts. It also provides tools for merging nodes, reordering atoms in a connected component, and renumbering atom serial numbers.
These checks help answer a useful question: is the structure merely untidy, or does it need repair? For example, adding hydrogens does not rebuild a missing loop. Likewise, a clash between side chains is not automatically fixed just because the structure has been validated. If side-chain clashes need attention, the Rotamers editor can change side-chain conformations using a backbone-dependent rotamer library.
Know when to use PDBFixer
If residues or atoms are missing, use the PDBFixer extension rather than treating the problem as routine cleanup. 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 remove water or heterogens and resolve alternate locations.
This distinction matters for protonation, too. SAMSON’s standard hydrogen addition places hydrogens at pH 7 for standard amino and nucleic acid residues, using valences for other structures. If your workflow requires a different pH, PDBFixer supports adding hydrogens at a specified pH. And although some workflows may require minimization after hydrogens are added, it is not universally necessary: the documentation notes that AutoDock Vina needs only polar hydrogens for determining hydrogen bonds.
A simple decision path
- Structure looks complete: use Home > Prepare for the cleanup steps you need.
- Unsure about geometry or naming: inspect the structure with Home > Validate.
- Missing residues, atoms, or pH-specific hydrogens: use PDBFixer and review its repair choices.
- Preparing many structures: the Batch Protein Prepare extension can process a folder or download structures from PDB identifiers.
This issue-first approach avoids doing unnecessary work and makes it easier to see which changes were made before docking, simulation, or analysis. For the full walkthrough and details of each option, read the protein preparation and validation tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.