A familiar challenge in molecular modeling is finding the same residue in two different representations. You may recognize a position in a protein sequence, then need to locate it in the structure—or select it in the 3D view and understand where it sits in the sequence. Switching between these views can make it easy to lose track of what you meant to inspect.
SAMSON’s Sequence View helps keep those representations connected. It is synchronized 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. That makes the sequence more than a reference strip; it can be a practical way to navigate the structure.
Use the sequence to locate and check selections
When you are working with a particular stretch of a protein, the sequence provides a direct place to make a residue selection. The synchronized views help you check where that selection appears in the document and in three dimensions. Conversely, when you select residues in the structure, the sequence gives you a way to see their position in the chain.
This back-and-forth is useful whenever the task involves both sequence context and structural context. For example, before continuing with a workflow that uses selected residues, you can use the sequence to make or review the selection, then look at the corresponding residues in the 3D Viewport. The key benefit is continuity: you do not have to treat the sequence and structure as separate, disconnected interfaces.
Color can help you scan patterns
Sequence Views can colorize residues according to biophysical properties, and those colors can be transferred to the corresponding residues in the 3D Viewport. This gives you another way to connect what you notice along the sequence with where those residues appear in the structure.
Color is most useful as a visual aid for scanning and comparison. Treat it as a cue for where to look, rather than as a substitute for checking the underlying property or interpreting the structure. Seeing the same coloring in the sequence and viewport can make it easier to follow a region as you move between representations.
Open the right sequence
There are two ways to open a Sequence View. 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 displays a pop-up so you can choose which sequence or sequences to view. This choice matters when you want to keep your attention on a particular chain: confirm that you are viewing the intended sequence before using it to navigate or interpret selections.
A simple sequence-to-structure routine
- Open the Sequence View from the Home menu or the structure’s context menu.
- If prompted, choose the chain or sequences you want to inspect.
- Select residues in the sequence, or select them in the Document View or 3D Viewport.
- Use the synchronized selection to check the corresponding residues across views.
- If useful, colorize residues by biophysical properties and view the transferred colors in 3D.
This routine is especially helpful when a modeling task depends on keeping a residue selection understandable as you move between a linear sequence and a spatial structure. For details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.