For molecular modelers, managing and understanding the complex structures of biological molecules can often feel overwhelming, especially when working with long chains or multiple biomolecules in a single environment. One of the challenges is visually intuiting important biophysical properties or selectively highlighting critical regions of a sequence and ensuring those modifications seamlessly reflect within a 3D workspace. If you’ve encountered this frustration, SAMSON’s interactive Sequence View might just be the solution you’ve been seeking.
The Sequence View in SAMSON serves as a powerful bridge between a molecule’s primary sequence and its 3D structure. Not only does this feature let you interact more intuitively with residues, but it also allows you to color-code residues based on their biophysical properties. All changes synchronize instantly between the sequence list and the 3D Viewport. For instance, selecting specific residues in the Sequence View automatically highlights and selects those same residues in the 3D structure, and vice versa. This cohesive synergy makes working with molecular designs far more manageable.
One standout feature is the ability to colorize residues. For example, you can assign color patterns to represent hydrophobicity, charge, or other biophysical attributes. Once applied, these personalized colorizations reflect directly within SAMSON’s 3D Viewport, enabling a quick and insightful visual analysis directly on the molecular structure.
Here’s how you can access and use Sequence Views effectively:
Opening Sequence Views
You can access the Sequence View using two simple methods:
- From the Home Menu: Navigate to the Home menu and select the View sequence option. This action opens the Sequence View and links it with the 3D Viewport.
- Through the Context Menu: Right-click on any structure in your workspace, select Structural model > View sequence, and the Sequence View for the selected structure will appear.
Handling Multiple Chains
When working with molecular structures that contain multiple chains, SAMSON offers flexibility. A dialog box appears, allowing you to select specific chains to examine in the Sequence View. This feature is particularly useful when focusing on distinct regions within large and complex systems.
Colorizing Residues
The beauty of Sequence Views lies in its colorization capabilities. Once your sequence is displayed, you can apply colors to different residues based on their biophysical properties. For instance, you might color charged residues in red and hydrophobic residues in blue. These colorizations can then be transferred directly to the 3D Viewport, enabling you to analyze interactions, patterns, or anomalies at a glance.
Such visualizations not only make your molecular modeling more intuitive but can also help identify critical insights, such as protein-ligand binding sites or favored interaction zones.
By leveraging Sequence View, molecular modelers can work more efficiently, transition seamlessly between sequence details and the 3D representation, and harness valuable visual tools for clearer insights.
To learn more about the Sequence View and its features, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at this link.