Anyone who models biomolecular systems knows how tedious it can be to manually pick specific residues in a 3D viewport. Whether you’re selecting residues for simulations, mutations, or analysis, navigating protein structures in 3D often leads to frustration—especially when chains overlap or residues are buried deep inside. Fortunately, SAMSON offers a solution: the Sequence View.
The Sequence View provides an interactive, one-dimensional representation of molecular sequences (proteins, nucleic acids, etc.) that is fully synchronized with both the 3D Viewport and the Document View. When you select a residue in the Sequence View, it is also selected in 3D—and vice versa.
Why use the Sequence View?
Here are just a few examples of why sequence-based selection is helpful:
- Residues hidden in 3D: Easily select residues that are buried in the protein core without struggling with the camera or transparency settings.
- Disambiguate repeating elements: With multiple chains that have similar sequences, the Sequence View helps you target the right one.
- Faster workflows: Selecting a range of residues is as simple as dragging your mouse across the sequence bar.
Going beyond selection: colorization
The Sequence View isn’t just for selection. You can also colorize residues based on their biophysical properties—hydrophobicity, polarity, etc. Even better, those colors automatically transfer to the 3D Viewport, giving you instant visual feedback in both views.
This lets you spot hydrophobic or hydrophilic regions in your structure at a glance and can be very useful for active site analysis or understanding protein folding patterns.
How to open the Sequence View
You can access the Sequence View in two ways:
- From the main menu: Go to the Home tab and click on View sequence.
- From the context menu: Right-click a structure in the Document View and choose Structural model > View sequence.
If you’re working with multi-chain structures, SAMSON prompts you to select which chains to visualize. That helps keep things tidy and focused.
Final thoughts
Sequence-based editing and visualization is a small but powerful improvement in molecular modeling workflows. It saves time, reduces error, and makes editing a more intuitive task—especially for users coming from bioinformatics backgrounds who think in terms of sequences rather than coordinates.
To learn more about the Sequence View in SAMSON, visit the official documentation: https://documentation.samson-connect.net/users/latest/sequence-view/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.