Molecular modelers working with complex biomolecules like proteins often struggle with keeping track of a structure’s hierarchy. Highlighting specific residues, examining chains, understanding the secondary structure, or quickly locating mutations or bound ligands — all of this can become very cumbersome when your only option is a 3D view.
The Sequence View in SAMSON makes this process much more manageable. It offers an intuitive, text-based way to explore biomolecular structures alongside the 3D viewer—helpful for selecting, navigating, and understanding molecular entities. If you’re new to the platform or haven’t yet explored this functionality, this post will show you why it’s worth incorporating into your workflow.
What Is the Sequence View?
As the name implies, the Sequence View displays the sequence of residues in your biomolecule. But it does more than just list residues: it aligns them by chains, annotates them with secondary structure information, and synchronizes your selection with the 3D model. This means that when you click on a residue in the sequence, it’s automatically selected in the 3D viewport—and vice versa.
Typical Use Cases
- Residue Selection: Need to mutate a specific amino acid or observe its environment? Click it directly in the Sequence View.
- Chain Overview: Proteins with multiple chains can be daunting to navigate. Sequence View breaks these down cleanly.
- Mutation Analysis: Comparing native and mutated structures becomes easier when relevant residues are visually aligned and accessible.
- Ligand Binding: Use the sequence-based insight to quickly check which residues lie near a bound molecule.
- Secondary Structure Reference: The view visually separates helices, sheets, and loops, which supports rational design decisions.
User Interface Highlights
The Sequence View pane appears in a tab typically located at the bottom of the interface, next to other viewers. The interface uses simple symbols and color codes to indicate residue type and structure. Clicking on a residue highlights it in the 3D model, and you can also right-click to apply further operations like selections, mutations, or visual tweaks.
Combined with SAMSON’s selection tools and Node Specification Language (NSL), you can craft highly specific selections directly through or in combination with the Sequence View. It allows for precision and clarity without needing to hunt and peck through the 3D model alone.
Why It Matters
When working with biomolecules, just having a 3D structure isn’t always enough. Being able to traverse the logical, sequential layout of residues adds another important layer of context—especially when dealing with mutations, comparing structures, or designing new molecular variants.
It’s a small feature that enhances both accessibility and precision, allowing you to work faster and more confidently, whether you’re a student learning structure or a researcher working on protein engineering.
To learn more about the Sequence View and other useful interface elements, visit the SAMSON Sequence View documentation page.
View full reference documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.