When dealing with large biomolecular systems like proteins, DNA, or RNA, molecular modelers often face a persistent challenge: navigating and selecting specific parts within increasingly complex structures. Whether you’re adjusting specific residues, analyzing subunits, or customizing visual representations, finding your way through densely packed 3D models can be frustrating and time-consuming.
This is where the Sequence view in SAMSON becomes especially helpful. It provides a compact, clear, and interactive representation of molecular structures through their sequences, allowing you to perform tasks faster, more accurately, and with more confidence.
What is the Sequence View?
The Sequence view is a visual interface in SAMSON that displays molecular sequences—such as amino acids in proteins or nucleotides in DNA/RNA—in a linear, text-style format. Each sequence corresponds to a chain, and clicking on residues selects them directly in the 3D model.
Why is it useful?
1. Simplifies residue-level manipulation: The traditional 3D view can be hard to work with when you need to isolate or edit specific residues. In the Sequence view, residues are laid out clearly and are selectable with a single click.
2. Enhances productivity: Instead of searching visually through complex spatial arrangements, you can skim through sequences quickly and make precise selections.
3. Enables advanced logic operations: Combine sequence selections with the Node Specification Language (NSL) to define selection criteria and filter structures by property, type, or location.
4. Great for education and communication: The Sequence view is intuitive for teaching biology and biochemistry, making it easier to explain structures to students or collaborators from non-technical backgrounds.
How to Access It
To open the Sequence view in SAMSON:
- Go to the main menu and click on Window > Sequence View.
- The panel will appear at the bottom or side of your workspace, depending on your layout settings.
- Use it to navigate, select residues, highlight chains, and more.
Real Use Case: Targeted Mutations
Imagine you’re studying a protein with over 300 residues and need to mutate residue 58 to test an electrostatic interaction. Instead of scrolling endlessly in 3D, open the Sequence view, locate residue 58 instantly, select it, and apply your mutation through SAMSON’s editing tools. The process takes seconds, not minutes.
Tips and Tricks
- Color-code different chains and residues to keep track of regions of interest.
- Combine views: Use the Sequence view alongside the 3D model to confirm selections visually.
- Use the context menu: Right-click on residues in the Sequence view to access additional tools such as selection expansion, isolation, and annotation.
By streamlining how you interact with biomolecular structures, Sequence view in SAMSON can significantly reduce workload and improve analytical focus. It’s a small change in interface—but a big improvement in workflow.
You can learn more by visiting the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.