When working with large biomolecular structures, one of the most frequent—and often frustrating—tasks is precisely selecting specific residues or residue ranges. Whether you’re defining regions for simulation, modifying part of a protein, or analyzing interactions, doing this in the 3D viewport alone can be cumbersome. Fortunately, SAMSON provides a feature that addresses this exact problem: the Sequence View.
Sequence View works hand-in-hand with the Document View and 3D Viewport. Selecting a residue in one view automatically selects it in the others, offering synchronized interactivity that makes structural exploration much smoother.
What Is Sequence View?
The Sequence View is an interactive visualization that displays the amino acid or nucleotide sequence(s) of the loaded molecular structure, right alongside the corresponding 3D model in SAMSON. This view lets you:
- Click to select residues or residue ranges directly from the sequence itself 🧬
- See selections highlight simultaneously in 3D
- Color-code residues based on biophysical properties, such as hydrophobicity or charge
Why Is This Helpful?
Selecting specific residues using the 3D model can be inaccurate and inefficient, especially for large proteins or when working at lower resolutions. With the Sequence View, you can:
- Precisely click on residue numbers or ranges without needing perfect camera angles
- Overlay visual cues like color based on properties to understand regions of interest
- Avoid multiple clicks or accidental selections in cluttered 3D environments
How to Launch the Sequence View
You have two quick options:
- From the Home Menu:
Click “View sequence” directly from the Home toolbar.
- From the Context Menu:
Right-click on any molecular structure, then select Structural model > View sequence.
Working with Multiple Chains
If your model has multiple chains (e.g., a protein complex, a dimer, or a heteromer), opening the Sequence View will prompt you to select which chain(s) to focus on. This saves visual space and helps you stay focused during analysis.
Bonus: Visualize Biophysical Properties with Color
The Sequence View is more than just a selection tool. You can easily color residues in the sequence based on their physicochemical traits, such as hydrophobicity or polarity. These color codes are instantly transferred to the 3D model, helping you identify functional regions.
This visual coding makes it much easier to understand structure-function relationships, recognize domain composition, or communicate findings to collaborators—especially those who aren’t comfortable working with atoms in 3D.
Conclusion
Whether you’re simulating active sites, analyzing mutations, or just trying to better understand the macromolecules you’re working with, the Sequence View in SAMSON gives you a faster, more intuitive, and more precise way to interact with molecular structures.
To explore this feature in more detail, visit the official SAMSON documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.