Two protein structures can share a meaningful local feature and still look poorly matched when you superimpose the entire molecules. A flexible domain, a changed loop, or simply differences elsewhere in the structure can distract from the region you actually want to compare. For molecular modelers, that can make a global overlay hard to interpret: is the site itself different, or is the rest of the protein shifting the picture?
A useful approach is to separate two questions: first, which residues correspond in the sequences? Then, how well do the structural regions you care about superimpose? In SAMSON, Protein Aligner lets you inspect sequence alignment and use selected residues as the basis for structural alignment.
Start with correspondence, not the overlay
Load the structures you want to compare, then open Home > Align to launch Protein Aligner. The tutorial demonstrates the workflow with hemoglobins 1DLW and 1RTX; the same steps can be applied to other proteins. If your structures contain solvent, ligands, or alternate locations that you do not want included in the comparison, clean them first using Home > Prepare.
Protein Aligner offers sequence alignment by structural model or by chain. The chain option is useful when a model contains multiple chains, such as in an oligomer. After generating the alignment, you can inspect corresponding residues and highlight properties such as similarity and polarity. This helps you identify a candidate region before judging its three-dimensional fit.
Hovering over a residue reveals its name and ID and highlights it in the molecular viewport. Clicking a residue selects it and its aligned partners. You can also select consecutive or non-consecutive residues using the keyboard modifiers shown in the interface. This link between the sequence view and the structure makes it easier to check that the residues you intend to compare are the ones you have selected.
Use a local region when the global fit is misleading
For a whole-protein superposition, leave residues unselected and click Align to this on the model you want to use as the reference. Protein Aligner then reports an RMSD on the other model’s button. That global fit is a useful overview, but it may not answer a region-specific question.
To focus on a local feature, select the corresponding residues in both aligned sequences, then click the alignment button beside the selection. In the tutorial, the first 20 residues are selected to compare two alpha-helices. The structures are superimposed using only those selected residues. This can make a local comparison easier to see when the overall proteins do not align closely.
Keep the scope of the result in mind: a fit based on selected residues describes that selection, not necessarily the agreement of the entire proteins. If you are comparing a binding site, helix, or other specific region, make sure the selection represents that question. It can also be helpful to compare the local fit with the whole-protein fit rather than treating either one as the only answer.
Make the comparison easier to read
After superposition, ribbons can help distinguish the structures. Use Visualization > Visual model > Ribbons; applying separate ribbon models to each selected structure lets you color them differently. You can toggle atomistic views using the checkboxes in Document view. These display choices do not change which residues were used for alignment, but they can make the overlay easier to inspect.
The key habit is to align for the question you are asking. Use sequence correspondence to choose a meaningful region, then use a selected-residue superposition to examine that region directly. For the full workflow and additional examples, see the Protein Aligner tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.