In molecular modeling, selecting specific residues in a large biomolecule can be tedious—especially when working directly in a dense 3D structure. Whether you’re prepping a simulation or trying to highlight particular regions, pixel-perfect clicking in the 3D Viewport just isn’t always practical. Fortunately, SAMSON’s Sequence View offers a way to interact with your model through a clean, intuitive sequence diagram that is directly synced with the 3D viewport.
The Sequence View provides a visual representation of the molecular sequence of your proteins or nucleic acids. Each residue is shown in linear order, and clicking on it instantly selects the corresponding atoms in the 3D Viewport and Document View. Likewise, selecting residues in 3D highlights them in the Sequence View. This bidirectional sync helps you work more efficiently—and avoid misclicking that tiny residue hidden behind a loop.
Why Use the Sequence View?
- Precise selection: Click on a residue name to instantly select it in 3D – no need to rotate endlessly to find it.
- Faster workflows: Selecting multiple residues or domains becomes far easier when you’re dealing with an unfolded linear view.
- Custom coloring: You can color-code residues based on biophysical properties, and these colors sync with the 3D model so structural analysis is visually reinforced.
How to Access the Sequence View
There are two main ways to open the Sequence View:
- In the top toolbar, go to the Home menu and click View sequence.
- Right-click on a structure in your Document View and navigate to Structural model > View sequence.
When working with structures that contain more than one chain, a dialog appears that lets you select exactly which chains you want to display.
When Does This Help Most?
If you frequently:
- Prepare simulations (e.g., selecting active sites or surface residues)
- Analyze mutations or sequence domains
- Color-code structural regions for presentations or publications
the Sequence View can be a big time saver. Plus, having the flexibility to switch between structure and sequence improves clarity and helps ensure accuracy.
Learn more in the official Sequence View documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.