For molecular modelers working with large biomolecular systems like proteins and nucleic acids, jumping between 3D structures and their primary sequences can often feel disjointed. Whether you’re selecting active sites, isolating chains, or analyzing mutations, a tool that bridges the gap between structure and sequence makes a big difference.
That’s where the Sequence View in SAMSON helps. This feature lets you interactively explore biomolecular sequences, select specific residues or chains, and immediately see how these selections relate to the 3D structure. It’s like having a map and your destination at the same time.
What is Sequence View?
Sequence View is a structured browser for the primary sequences of biomolecules loaded in SAMSON. It gives you a compact, quick-access panel that displays the amino acid or nucleotide sequences of all relevant chains. Each chain is labeled and you can navigate around multi-chain complexes without getting lost in the complexity.
How Sequence View Helps in Practice
Here are some common scenarios where Sequence View saves time and effort:
- Selecting specific residues: Click directly on residues or use selection tools within the Sequence View. The corresponding atoms light up in the 3D view.
- Identifying and highlighting mutations: When working with variants or mutant libraries, scrolling through sequences becomes essential. Sequence View enables you to quickly pinpoint these differences.
- Chain-specific analysis: Large complexes may contain multiple chains. Sequence View keeps things manageable by separating sequences chain-wise for quick navigation.
- Advanced selections: You can combine Sequence View with the Node Specification Language (NSL) for refined selections based on residue types, names, and more.
Tips to Use Sequence View Effectively
If you’re just getting started with Sequence View, here are a few practical tips:
- Keep it docked: Dock the Sequence View in your interface to monitor sequence details while you’re modeling in 3D.
- Use it together with Selection Editors: Combining tools like the Node Editor or Geometry Inspector with Sequence View offers more precise control.
- Explore mutations visually: When comparing wild-type and mutant structures, use Sequence View to highlight changes and observe structural consequences instantly.
Why It Matters
Many molecular modelers still switch back and forth between external sequence viewers and 3D modeling software. That back-and-forth is not only time-consuming but discourages interactive exploration. By integrating both in one interface, Sequence View makes that process seamless and efficient. It encourages users to explore both structural and sequence-based perspectives simultaneously, accelerating hypothesis generation and validation.
Ready to enhance your molecular modeling workflow with Sequence View? Learn more in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.