When working with complex biomolecular systems, even seasoned modelers can find themselves buried in a tangle of atoms, chains, and residues. Whether you’re analyzing a mutated protein or editing sequences interactively, it’s easy to lose track of where you are in the structure. Fortunately, SAMSON provides a helpful feature tailored to this: the Sequence View.
The Sequence View offers a clean, detailed representation of the molecular sequence you’re working with, directly within the SAMSON interface. If you’re exploring structural mutations, investigating active sites, or simply trying to get an overview of your macromolecule, this tool can simplify your workflow considerably.
Why Sequence View Matters 🧬
Unlike purely visual molecular renderings, a sequence-based view of your structure allows you to:
- Quickly identify specific residues or nucleotide bases
- Navigate to structural motifs or functional regions
- Assess mutations or binding sites with precision
- Select and edit fragments by clicking directly in the sequence
This significantly reduces the amount of guesswork involved when exploring or modifying a structure, especially in large molecules such as proteins, RNA, or DNA complexes.
What You’ll See
Once enabled, the Sequence View panel displays your molecule as a series of chains and residues:
- Residues are color-coded for readability
- Hovering over elements highlights them in the 3D view
- Clicking a residue selects it, both in the panel and 3D scene
This dual correspondence between the sequence and 3D spatial layout makes it intuitive to isolate specific regions or chains in your molecule. For instance, if you’re studying the mutation of a serine to a glycine at position 92, you can find and click on it immediately in the sequence view, then apply any edits or analysis tools needed.
When to Use It
This panel is particularly useful when:
- You are manually annotating or modifying structures
- You want to understand the folding or grouping of residues
- You wish to align sequences with known structures or motifs
For example, if you’re developing a sequence-based mutation study or designing an inhibitor targeting a particular active site, this feature provides an efficient starting point.
No Setup Required
The best part? The Sequence View is integrated within SAMSON and works right out of the box. There’s no need to install any extra extensions to enable this feature. It’s part of what makes SAMSON valuable for structural analyses beyond pure visualization.
Learn More
If you’re ready to explore how the Sequence View can make your modeling tasks faster and more precise, check out the official SAMSON documentation for more details: Sequence view documentation.
To browse through all available reference pages, including this one, visit the main documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.