When working with large biomolecular structures, navigating through multiple chains and understanding their sequences in detail can quickly become overwhelming. Whether you’re inspecting interface residues or preparing a system for simulation, having a fast and intuitive way to examine individual chains is a time-saver. Sequence Views in SAMSON provide an effective bridge between the 3D structure and its corresponding sequence, especially when dealing with structures that contain several chains.
For molecular modelers juggling multimeric proteins, viruses, or protein complexes, pinpointing which residue belongs to which chain directly in a 3D model takes time and effort. This is where SAMSON’s pop-up dialog to open specific chains in the Sequence View is especially practical.
Quick Access to Chain Sequences
There are two intuitive ways to open the Sequence View:
- From the Home menu via the View sequence button.
- By right-clicking on a structure and selecting Structural model > View sequence in the Context menu.
If your structure contains multiple chains, instead of opening all of them at once or forcing you to scroll through a long concatenated sequence, SAMSON opens up a pop-up dialog that lets you choose the sequence(s) you want to view.
Why This Matters
This might seem like a small detail, but being able to isolate and focus on specific chains enhances model comprehension, reduces visual clutter, and supports structure-specific manipulations such as residue colorization or mutation planning. It also simplifies collaborative discussions—when you share your screen or snapshots, you can be sure that you’re zooming in on just the region or chain of interest.
Complement 3D with Sequence Insight
Once a chain is selected and its Sequence View is opened, the view remains synchronized with the 3D viewport. Selecting a residue highlights it both in the sequence and the molecular model. This consistency is helpful when validating modeling steps, inspecting docking results, or preparing visual material for presentations and publications. No need to guess—just select and see.
Conclusion
Sequence Views are more than just a visual aid. The ability to select specific chains prevents distraction and gives clarity when you need it most. It’s one of those thoughtful interface features that keeps your focus where it belongs: on the molecular insights, not the UI.
To learn more and explore other features of the Sequence View, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.