A molecular structure can be easy to inspect in 3D and still be difficult to reason about residue by residue. You may know which part of a protein sequence matters, but finding that same residue in a crowded structure can interrupt the work. Or you may select a region in the 3D model and want to understand where it sits in the sequence.
SAMSON’s Sequence View helps connect those perspectives. It stays synchronized with the document: selecting residues in the sequence selects them in the Document View and 3D Viewport, and selections made in those views are reflected in the sequence. That makes the sequence a practical navigation tool—not just a separate display of letters.
Use the sequence to locate structure
When you are working from a sequence-level observation, open the Sequence View and select the residue or residues you want to inspect. The corresponding selection appears in the other synchronized views, so you can move from sequence context to structural context without having to identify the same location manually in 3D.
This is useful when you want to keep track of which part of the model you are examining while moving between representations. The sequence provides an ordered view of residues; the 3D Viewport provides their spatial arrangement. Synchronization lets you use both views as parts of one workflow.
Use the structure to locate sequence
The same connection works in the opposite direction. If you select residues while inspecting the structure, their corresponding positions are selected in the Sequence View. This can help answer a simple but important question: “Which part of the sequence am I looking at?” It also gives you a way to check that a structural selection corresponds to the region you intended to examine.
For a focused workflow, start with either view, make a selection, and check the synchronized selection in the other. You can then continue inspecting the model with the sequence position in view, or return to the structure with the selected residues identified.
Color can carry context into 3D
Sequence Views can colorize residues based on biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This provides another way to connect sequence-level information with the structure: instead of relying only on a selection, you can use color to see the property-based pattern across the model.
Colorization is especially helpful when you want to inspect a pattern across multiple residues rather than focus on one selection at a time. The sequence view shows the pattern in residue order, while the 3D view shows where those residues lie in space. The two views offer complementary ways to examine the same model.
Opening the right sequence
To open a Sequence View, choose View sequence from the Home menu. Alternatively, right-click a structure and choose Structural model > View sequence from the context menu.
If the structure contains multiple chains, SAMSON displays a pop-up that lets you choose which sequence or sequences to view. Take a moment to select the relevant chain or chains before starting your sequence-based inspection. This keeps the view aligned with the part of the structure you mean to work on.
The practical takeaway is simple: when switching between residue order and 3D arrangement, use synchronized selection to preserve context, and use sequence colorization when a property pattern is more useful than a single highlighted selection. Learn more in the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.