When analyzing biomolecular structures, a common frustration is keeping selections consistent across different representations of your model. If you select a residue or chain in a 3D viewport, it can be tedious to track it back to its sequence position—or vice versa.
This is where the Sequence View in SAMSON comes in. Designed to streamline navigation and selection, the Sequence View provides a synchronized, interactive way to explore residue sequences directly alongside your structural model.
Why use a sequence view?
Many molecular modelers need to analyze or manipulate specific regions of macromolecules. Selecting these regions from a 3D structure can be error-prone and inefficient, especially for large and complex systems. The Sequence View links directly to the 3D viewport and the Document View—selecting a residue in one view automatically highlights it in the others.
Live highlighting between sequence and structure
This interactivity means you can quickly understand how the sequential information maps onto the 3D structure. For example, identifying the residues of a binding site in the sequence allows you to immediately see and manipulate them in 3D.
Biophysical insights through color
Beyond selection, the Sequence View includes colorization options that highlight residues based on biophysical properties. These colored representations are reflected in the 3D viewport, helping you spot patterns—like hydrophobic regions or charged residues—at a glance.
How to access the Sequence View
You can open the Sequence View easily in two ways:
- Click on View sequence in the Home menu.
- Right-click on a structure in the Document View or Viewport and go to
Structural model > View sequence.
Working with multi-chain structures
When working with multi-chain models, SAMSON prompts you to select which chains to display sequences for. This prevents unnecessary clutter while still giving you full control over your analysis scope.
Overall, the Sequence View is a straightforward but effective tool for bridging the gap between sequence and structure in molecular modeling. Whether you’re inspecting a specific residue or analyzing entire chains, this synchronized interface saves time and reduces confusion.
To learn more, visit the Sequence View section of the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.