A familiar challenge in molecular modeling is losing track of where a residue sits. You may recognize a position in a protein sequence, then need to find the corresponding part of the structure—or select something in the 3D view and identify it in sequence context. Switching between views can make that simple task feel harder than it should.
SAMSON’s Sequence View helps bridge that gap. It is synchronized with the document: selecting residues in the sequence selects them in the Document View and the 3D Viewport, and selections made in those views are reflected in the sequence. That connection makes the sequence useful not just for reading, but also for navigating and checking what you have selected.
A practical way to move between sequence and structure
When you know a residue or region from the sequence, start by opening the Sequence View and selecting the relevant residues there. Then look at the synchronized selection in the 3D Viewport to see where it lies in the structure. Going in the other direction works too: select residues in the structure and use the sequence view to see their position in sequence context.
This back-and-forth is useful when you want to verify that a selection corresponds to the region you intended before continuing with a structural workflow. It also gives you two complementary ways to inspect the same selection: the sequence provides linear context, while the 3D Viewport shows the residues in their spatial arrangement.
Make sequence patterns easier to inspect
Sequence Views can colorize residues according to biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This gives you a way to carry a sequence-based visual cue into the structural view, rather than treating the sequence and structure as separate displays.
A useful habit is to decide what you want to compare before applying color: for example, whether you are trying to notice a property across the sequence or see where those colored residues occur in the structure. Color is a visual aid, not a substitute for checking the selection and its structural context. Because colors can be transferred to the 3D Viewport, you can inspect the same visual cue in both places.
Open the view for the structure you need
There are two documented ways to open a Sequence View. From the Home menu, choose View sequence. 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 so you can choose which sequence or sequences to view. Take a moment to make that choice deliberately: viewing the intended chain helps keep sequence-based selections aligned with the structure you are examining.
Keep the two views working together
The main benefit is a more direct route between a residue’s place in a sequence and its location in a molecular structure. Open the Sequence View for the structure, choose the appropriate chain when prompted, and use synchronized selection to move between sequence context and 3D context. When a biophysical property is relevant to your inspection, colorize the sequence and transfer those colors to the structure.
For more details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.