A whole-protein superposition can be useful—but it can also obscure the part you actually care about. Two proteins may share a similar helix, binding-site region, or other selected segment while differing elsewhere. When the entire structure is used for alignment, those differences can make the region of interest appear poorly matched.
A practical solution is to align the structures using only corresponding residues from that region. This keeps the question focused: instead of asking how well the complete proteins overlap, you ask how well a specific part can be superimposed.
Start with the sequence correspondence
In SAMSON, open Home > Align to launch Protein Aligner. Load the structures you want to compare first. The tutorial demonstrates the workflow with hemoglobins 1DLW and 1RTX, but you can apply the same steps to your own proteins.
Generate a sequence alignment using either Align sequences (by structure) or Align sequences (by chain). The first compares structural models; the second aligns individual chains, which is useful when a model contains multiple chains. The alignment provides a way to identify corresponding residues before choosing a region for structural comparison.
You can inspect residue correspondence directly in the alignment. Hovering over a residue shows its name and ID and highlights it in the viewport. Clicking a residue selects it and its aligned partners. This connection between the sequence view and the 3D structure helps you check that the residues you intend to compare are the ones being selected.
Use a local region to guide the superposition
For a whole-protein superposition, make sure no residues are selected, then click Align to this on the row of the model you want to use as the reference. Protein Aligner reports an RMSD for the other model after the superposition.
For a region-specific comparison, select the corresponding residues in both sequences instead. In the tutorial, the first 20 residues are selected because the two N-terminal alpha-helices look similar but do not align well in the whole-protein view. Once the relevant residues are selected, click the alignment button beside that selection. The structures are then superimposed using only the selected residues.
The important distinction is what drives the fit: no selection gives you a whole-protein alignment, while a selection lets you focus the structural comparison on that region. This is useful when a local motif or segment is the subject of your analysis and the rest of the protein would distract from that comparison.
Make the selection deliberate
Before applying a local alignment, confirm that the residues selected in each sequence represent the corresponding segment you want to compare. Protein Aligner supports selecting multiple consecutive residues with Shift, non-consecutive residues with Ctrl or Cmd, and removing residues from a selection with Alt. You can also select residues in the document view or viewport; aligned residues are highlighted in Protein Aligner.
After the superposition, inspect the structures in the viewport to see how the chosen region overlaps. If secondary structures are not visible, SAMSON’s Visualization > Visual model > Ribbons option can make them easier to inspect. Separate ribbon models can be created for each protein to distinguish them visually.
Local alignment does not replace whole-protein comparison; it answers a narrower question. Using both views can help you distinguish a globally similar pair from proteins that share a well-matched region despite differences elsewhere.
For the complete workflow and additional examples, see the Protein Aligner tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.