A molecular structure can be easy to inspect in 3D and still be difficult to navigate residue by residue. When you need to locate a particular part of a protein, the sequence gives you a readable map—but switching back and forth between that map and the structure can make it harder to keep your place. SAMSON’s Sequence View helps address this by keeping sequence selection synchronized with the Document View and 3D Viewport.
Select residues in the Sequence View and they become selected in the other views; select them in the Document View or 3D Viewport and the sequence selection updates as well. That two-way connection is useful when your task moves between sequence-level questions and spatial inspection. You can start with a region in the sequence and see its corresponding selection in the structure, or begin with a selection in the structure and find the residues in sequence context.
A practical way to move between sequence and structure
Imagine that you are inspecting a structure and want to understand where a selected set of residues sits in the sequence. Open the Sequence View and use the synchronized selection to connect what you see in the viewport with its place in the sequence. The reverse is just as useful: select residues in the sequence, then inspect their selection in 3D to regain spatial context.
This can make routine navigation less error-prone. Rather than relying only on memory while switching between a linear sequence and a three-dimensional model, you can use the shared selection as a visual reference. It is especially helpful when you are checking a region, comparing sequence position with structural location, or preparing to use selected residues in a later structure workflow.
Open the view from the place that suits your workflow
You can open a Sequence View in either of two ways. From the Home menu, choose View sequence. Or, right-click a structure and choose Structural model > View sequence from the context menu. If the structure has multiple chains, SAMSON presents a dialog so you can choose which sequence or sequences to view.
For a structure with several chains, pausing at this choice is worthwhile: it lets you focus the sequence display on the chain or chains relevant to the question you are investigating, instead of treating the model as one undifferentiated sequence.
Use color as an additional guide
Sequence Views can also colorize residues according to biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This adds a visual cue alongside selection: the sequence can help you read the residue pattern, while the viewport shows where the corresponding residues lie in the model. Color is most useful as a complement to selection, not a replacement for checking which residues are actually selected.
The central idea is simple: keep the sequence and structure in the same conversation. When navigating feels like a repeated search between two different representations, a synchronized selection provides a direct connection between them. For details on opening and using the view, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.