When working with a molecular structure, it is easy to lose track of where a residue sits in the sequence. A position that looks obvious in a 3D view can be harder to identify in a long chain, while a sequence position alone may not tell you where to look in the structure. Switching between these representations can interrupt a modeling workflow and make it harder to check that you are working with the intended residues.
SAMSON’s Sequence View helps connect those two ways of looking at a molecule. It stays in sync with the document: selecting residues in the sequence also selects them in the Document View and 3D Viewport, and selections made in those views are reflected in the sequence. Instead of treating the sequence and structure as separate places to inspect, you can use them together to locate and verify a selection.
A practical selection workflow
Start with the view that makes the target easiest to recognize. If you know the residue from its place in the sequence, use the Sequence View to select it. Then check the corresponding selection in the 3D Viewport. If you first spot a region in the structure, select it there and use the synchronized sequence view to see which residues are involved.
This back-and-forth is useful as a simple verification step. Before continuing with a structure workflow, confirm that the highlighted residues in the sequence match the region you intended to select in 3D. When the target is easier to identify in one representation than the other, the synchronized selection lets you use that advantage without losing the connection between them.
Sequence View can also help when selection is only the beginning of the task. The documentation describes using selected residues in downstream structure workflows. Keeping the sequence and structure views in sync can make it easier to check the selection before moving on to those next steps.
Use color to make sequence patterns easier to scan
Colorization adds another way to inspect a sequence. Sequence Views can color residues according to biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This gives you a way to compare a property-based view of the sequence with the arrangement of the same residues in the structure.
Color is most useful as a visual aid: it can help you notice and follow differences across the sequence, and then locate those residues in 3D. Treat the colors as a way to organize what you are looking at, not as a substitute for interpreting the underlying molecular information. The important practical benefit is continuity: the sequence and structure can show the same residue selection and color pattern.
Open the right sequence
There are two ways to open a Sequence View. Choose View sequence from the Home menu, or right-click a structure and choose Structural model > View sequence from the context menu. If the structure contains multiple chains, SAMSON presents a pop-up so you can choose which sequence or sequences to view.
That chain choice is worth making deliberately: it helps ensure you are inspecting the sequence relevant to the structure region you are working on. Once the view is open, use selection synchronization to move between sequence-level identification and structural context, and use colorization when a property-based visual cue would make the residues easier to scan.
For more details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.