A common frustration in molecular modeling is losing the connection between a residue’s place in a sequence and its location in a three-dimensional structure. A sequence is easy to scan, while a structure is easier to inspect spatially—but switching between the two can make it difficult to keep track of what you are looking at.
SAMSON’s Sequence View helps bridge that gap. It stays synchronized with the Document View and the 3D Viewport: select residues in the sequence and they are selected in the other views; select them in the Document View or 3D Viewport and the corresponding residues are selected in the sequence.
Use the sequence as a navigation aid
When you are inspecting a model, it can be useful to begin with the sequence rather than trying to identify a residue directly in the 3D scene. The sequence gives you a linear view of the residues. Once you select a residue there, the synchronized selection shows you where it is represented in the other views. This makes it easier to move between a sequence-level question and a structural inspection without treating them as separate tasks.
The synchronization also works in the opposite direction. If you select residues while working in the Document View or 3D Viewport, the matching selection appears in the Sequence View. That can help when you have already found a region in the structure and want to understand where it sits in the sequence.
Open the right sequence
There are two ways to open a Sequence View:
- Choose View sequence from the Home menu.
- 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 so you can choose which sequence or sequences to view. This is a useful moment to check that you are opening the chain relevant to your current task, especially when a model contains several chains and you are comparing a particular region.
Bring sequence color into the 3D view
Sequence Views can also colorize residues according to biophysical properties. The colors can then be transferred to residues in the 3D Viewport. This gives you a way to carry a sequence-based visual cue into the structure, where you can inspect the colored residues in their spatial context.
A practical way to use this feature is to treat the sequence and the 3D model as complementary views: use the sequence to locate or colorize residues, then inspect the corresponding residues in the viewport. If you start from the structure instead, select the region there and use the synchronized sequence selection to see its position in the linear view. The documentation describes colorization based on biophysical properties, but the colors should be treated as visual cues to support inspection—not as a replacement for interpreting the underlying model and data.
A simple workflow to try
- Open a structure’s Sequence View from the Home menu or its context menu.
- If prompted, choose the chain or sequences you want to inspect.
- Select residues in the sequence and look for the corresponding selection in the 3D Viewport.
- Or select residues in the structure and use the sequence view to locate them in the chain.
- When useful, colorize residues by biophysical properties and transfer those colors to the 3D Viewport.
The result is a more direct route between “where is this residue in the sequence?” and “where is it in the structure?”—a small change in how you navigate that can make structural inspection feel much less like keeping two maps in your head.
For details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.