For many molecular modelers, managing complex biomolecular systems means jumping between multiple representations: 3D structures, sequences, and data tables. A frequent source of friction is the disconnect between these representations—particularly when selecting elements in one view doesn’t immediately reflect in others. This slows down workflows, introduces errors, and makes it harder to stay focused on design or analysis goals.
The Sequence View in SAMSON provides a way to relieve this friction. It offers a synchronized environment where selections made in the sequence are automatically reflected in the 3D viewport and Document View, and vice versa. This article walks through the essential capabilities of this feature and shows how it can help you stay coordinated when working with large macromolecular structures.
What is the Sequence View?
The Sequence View is an interactive panel that displays the linear sequence of residues in your selected structure. Beyond just viewing, it allows you to interact with your molecule by selecting amino acids or nucleotides directly in the sequence. When you click on a residue, the selection carries over to both the 3D Viewport and the Document View. This synchronization works in all directions—select something in the 3D View, and it’s highlighted in the sequence.
Color-Coding Residues Based on Biophysical Properties
One particularly useful feature is the ability to color residues based on their biochemical or biophysical properties. These color codes help you instantly recognize the nature of different regions—such as hydrophobicity or charge—within your sequence and see how they map onto the full 3D structure.
Even better: the colorization done in the Sequence View automatically propagates to the 3D Viewport. This means you can visually analyze the chemical context of your macromolecule without flipping between views or reapplying the same style settings multiple times.
Opening the Sequence View
You can access the Sequence View in two ways:
- Click View sequence in the Home menu.
- Right-click on a structure in the Document View and choose Structural model > View sequence.
Working with Multi-Chain Structures
If your structure includes multiple chains, SAMSON doesn’t overwhelm you. A pop-up dialog lets you select which sequences to display, so you can focus on the parts you care about.
Why It Matters
By keeping your sequence and structure data in sync, the Sequence View helps reduce cognitive load and speeds up editing and analysis tasks. Whether you’re performing mutational studies, aligning sequences, or just trying to figure out “what residue is that spike again?”, synchronized interaction makes it easier to stay oriented in complex molecules.
To learn more about the Sequence View, visit the original documentation page here: https://documentation.samson-connect.net/users/latest/sequence-view/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.