When working with complex macromolecular structures, especially those containing multiple chains, it can be challenging to quickly identify and select residues of interest or detect structural differences across chains. Whether you’re comparing active sites, tracing mutations, or analyzing binding interfaces, managing multi-chain structures efficiently is key.
That’s where the Sequence View in SAMSON comes in. It offers an intuitive way to interact with and visually analyze sequences of molecular structures. In this post, we’ll focus on a helpful feature: how Sequence View handles structures with multiple chains, and how this can streamline your modeling workflow.
Why multiple chains are a pain
In many molecular modeling tasks, such as protein-protein docking, antibody modeling, or multimeric enzyme analysis, you’re often dealing with structures containing multiple polypeptide chains. Managing chain-specific information — like identifying a particular residue in chain B versus chain A — can quickly become tedious in a 3D viewport alone.
Sequence View simplifies this task by giving you synchronized access to residue-level information across all relevant views: the sequence, structure, and document hierarchy.
Chain selection when opening Sequence View
When you activate the Sequence View on a structure containing multiple chains, SAMSON automatically prompts you to select which chains to visualize. This small but powerful feature helps you focus only on what matters for your current task without cluttering your workspace.
You can either select individual chains or view all chains at once, depending on what you need. This interactive selection makes it easy to compare chains side-by-side using color-coded views and directly synchronize them with the 3D viewport.
Two ways to open the Sequence View
SAMSON provides two main ways to access this feature:
- From the Home menu: Click on View sequence to activate the Sequence View for the selected structure.
- From the Context menu: Right-click on a structure, then go to Structural model > View sequence.
Both methods will trigger the chain selection dialog if your structure contains multiple chains. This ensures you always retain control over what is displayed — and more importantly, what isn’t.
Interactively linked views
The Sequence View is synchronized with the 3D Viewport and the Document View, so selections you make in one are reflected live in the others. This is particularly useful for inspecting homologous residues across chains or visually tracking sequence variations in symmetric assemblies or oligomeric constructs.
Conclusion
If you’ve ever struggled to manage large or complex molecular assemblies, especially those with multiple chains, give Sequence View a try. The integrated chain selection dialog can save time and reduce confusion, letting you focus on your scientific questions rather than interface navigation.
📖 Learn more about this feature in the full documentation: Sequence View – SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.