A familiar challenge in molecular modeling is knowing exactly where a residue in a protein sequence sits in the three-dimensional structure. A sequence is compact and easy to scan, while a structure reveals spatial context—but switching between them can make it difficult to keep track of which part you are inspecting. Select the wrong residue, or lose your place while moving between views, and even a small analysis can become unnecessarily frustrating.
SAMSON’s Sequence View helps connect these two ways of looking at a molecular structure. It stays in sync with the document: selecting residues in the sequence also selects them in the Document View and the 3D Viewport, and selections made in those views are reflected in the Sequence View. That means you can use the sequence to find a region, then look at the corresponding selection in the structure without having to translate between separate lists by hand.
Open the sequence for a structure
There are two 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. The context-menu route can be convenient when you are already working with a particular structure in the document.
If the structure contains more than one chain, SAMSON displays a pop-up so you can choose which sequence or sequences to view. This is a useful moment to orient yourself: decide whether you need to inspect one chain or compare multiple chains, then make your selection.
Use selection as a navigation bridge
Once the sequence is visible, selecting residues there gives you a direct way to locate the same residues in the Document View and 3D Viewport. The reverse is useful too: select residues while exploring the structure, then use their selection in the sequence as a reference for where they fall along the chain. This shared selection state is especially helpful when a structural question starts in one view but needs to be checked in another.
For example, you might first notice a region while inspecting the 3D structure, then look at its position in the sequence. Or you might begin with a sequence region you want to inspect and use the synchronized selection to find it in three dimensions. In either direction, the key benefit is a consistent selection—not an extra step of manually identifying the same residues in two different representations.
Bring sequence color into the 3D view
Sequence View can also colorize residues based on biophysical properties, and those colors can be transferred to residues in the 3D Viewport. Color can provide another visual cue when moving from a linear sequence to a spatial structure: instead of relying only on residue names or selection, you can view the corresponding color pattern in the molecular context.
A practical way to use the feature is to open the sequence for the structure you are studying, select or inspect a region in the view that best suits your current task, and then check the synchronized selection in the other views. If a colorized sequence is useful for your analysis, apply the available colorization and transfer the colors to the 3D representation. These connections make it easier to keep sequence position, residue selection, and structural context together as you work.
To learn more about opening and using Sequence Views, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.