Molecular modelers often deal with complex biomolecular systems made of long sequences of residues spanning multiple chains. One common challenge is maintaining clarity when switching between views: sequences, 3D models, and structural hierarchies. SAMSON addresses this issue with the Sequence View, offering a synchronized and interactive way to navigate and analyze molecular structures.
This feature is especially useful when you want to do any of the following:
- Quickly identify and select specific residues in long sequences
- See where mutations, modifications, or specific regions map in 3D space
- Color-code sequences by biophysical properties and immediately view these changes in the 3D model
How Sequence View Helps
In SAMSON, the Sequence View is more than just a linear representation of amino acid or nucleotide chains. It’s synchronized with the Document View and the 3D Viewport, so interacting with residues in one view immediately updates the others. This tight integration speeds up your workflow and reduces errors when interpreting data or preparing figures for publications.
Want to look at a particular loop region or a mutation hotspot? You can click on the residues in the Sequence View and instantly see them highlighted in the 3D model. Conversely, selecting a region in the 3D viewport shows you exactly where you are in the sequence — no guesswork involved.
Highlight by Biophysical Properties
One standout feature is the ability to colorize sequence residues based on their biophysical or chemical properties. This is especially valuable when analyzing features such as hydrophobicity, charge distribution, or secondary structure content. These color codings are not isolated — they also appear in the 3D Viewport, making structural interpretation visually intuitive.
Accessing the Sequence View
You can bring up the Sequence View in two ways:
- From the Home menu: Click the View sequence button to open the view.
- From the Context menu: Right-click on the structure in the Document View, hover over Structural model, and select View sequence.
If your structure includes multiple chains, SAMSON will prompt you to choose which sequences to display. This ensures your workspace stays organized, and you only focus on the chains you’re analyzing.
Why It Matters
Whether you’re tracking mutations, studying domain boundaries, or preparing annotated 3D models, synchronized sequence interaction can make a real difference. With SAMSON’s Sequence View, you don’t have to switch tools or rely on external scripts to compare sequence and spatial data. Everything you need is woven into a single, cohesive environment.
Want to dive deeper? Explore the full documentation on the Sequence View 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.