For molecular modelers working with large biomolecular structures, navigating between residues in 3D can quickly become a tedious task. Zooming, panning, rotating – and still not finding that specific residue you were looking for. Sound familiar?
Fortunately, SAMSON offers a helpful tool that many users overlook: the Sequence View. It lets you inspect and interact with molecular sequences, and it’s synchronized in real time with both the Document View and the 3D Viewport. This means that when you select a residue from the sequence, it gets selected in the 3D structure – and vice versa. No more guesswork or manual searching!
See the full sequence at a glance
The Sequence View displays residues in a linear layout, making it particularly helpful for exploring proteins, DNA, or RNA. It helps you:
- Quickly locate specific residues across chains
- Select multiple residues with ease
- Monitor structural features along a chain
How to open the Sequence View
There are two simple ways to access the Sequence View in SAMSON:
- From the Home menu, use the View sequence command:
- Right-click on any structural model in the Document View, and select Structural model > View sequence:
If your molecular structure has multiple chains, SAMSON will ask which one(s) you want to open:
Why use Sequence Views?
Besides simplifying selection, the Sequence View also provides powerful visual features. One particularly useful feature is colorization based on biophysical properties. You can visualize hydrophobicity, charge, or other properties directly on the sequence – and apply these colors to the 3D structure with a single click:
This can help you quickly assess regions of interest, highlight potential binding pockets, or better understand sequence-structure relationships – especially for those who prefer a top-down view of molecules, before diving into 3D.
Efficient exploration through integration
What makes the Sequence View especially useful is its full synchronization with SAMSON’s other views. Selecting residues in the Sequence View updates the Document View and highlights corresponding atoms in 3D. This bidirectional connectivity provides a consistent experience, reducing mistakes and making structure analysis smoother.
If you’ve been relying on visual inspection alone to traverse long protein chains or nucleic acid segments, give the Sequence View a try. It might just save you a lot of time – and clicks.
To learn more, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.