A familiar challenge in molecular modeling is keeping track of where a residue sits in the sequence while also understanding where it sits in the structure. Moving back and forth between a linear sequence and a three-dimensional model can interrupt the work—and make it harder to focus on the region you actually want to inspect.
SAMSON’s Sequence View helps connect those two perspectives. It stays in sync 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 View. Instead of treating sequence and structure as separate tasks, you can use them together while exploring a model.
Open the sequence for the structure you are working on
You can open a Sequence View from either of two places. 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 contains multiple chains, SAMSON presents a dialog so you can choose which sequence or sequences to view. That choice matters when you are trying to relate a particular part of a model to its sequence: first decide which chain is relevant to the question you are investigating, then open the corresponding view. When several chains are relevant, you can choose multiple sequences instead of treating the structure as though it had only one.
Use selection to maintain context
Once the Sequence View is open, select residues in the sequence to see the corresponding selection in the Document View and 3D Viewport. You can also make a selection in the other direction: select residues in the document or 3D view and see that selection reflected in the sequence. This two-way connection is useful when you know the region by its position in one view but need to identify it in another.
For example, you might begin by locating a residue in the sequence, then use the synchronized selection to find its position in the model. Or you might select a region while inspecting the 3D structure and use the Sequence View to see where that selection falls in the sequence. In either case, the sequence and the structure remain connected through the selection, helping reduce the need to mentally reconstruct that relationship while switching views.
Make sequence patterns easier to scan
Sequence Views can also colorize residues according to biophysical properties. Color can make a sequence easier to scan for patterns, and those colors can be transferred to the residues in the 3D Viewport. This gives you another way to compare a sequence-level view with the spatial arrangement of the same residues. The colorized view is not a substitute for checking the structure; it is a visual aid that brings the two representations into closer conversation.
A practical way to use the feature is to open the sequence for the structure or chain you are examining, make a selection in whichever view is most convenient, and use the synchronized selection to follow that region in the other views. If a sequence-level color pattern is useful for your question, apply colorization and transfer it to the 3D structure for spatial context.
This workflow is especially helpful when the difficulty is not finding a particular representation, but keeping sequence and structure aligned as you explore. The Sequence View gives you a direct bridge between them—through shared selection and, when useful, shared color.
For more details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.