One of the essential challenges in molecular modeling is efficiently selecting and managing residues across various views of a molecular structure. Whether you are analyzing a protein sequence, refining structural models, or applying specific visual styles to residues, maintaining synchronization between sequence and 3D structures is crucial. Fortunately, SAMSON’s Sequence View offers a seamless solution for this.
With the interactive Sequence View in SAMSON, selecting residues becomes highly streamlined and intuitive. Residues selected in the Sequence View automatically become selected in the Document View and the 3D Viewport, and vice versa. This level of synchronization ensures that you no longer need to tediously switch between different views to cross-check your workflow.
Here are some practical ways you can make the most out of this feature:
How to Access the Sequence View
Getting started with the Sequence View is simple. You can access it in two ways:
- From the Home menu, click on the View sequence command:
- Alternatively, right-click on a structure and select Structural model > View sequence from the Context menu:
Handling Structures with Multiple Chains
If your molecular structure contains multiple chains, SAMSON offers an intuitive solution to select which sequence(s) to display. Upon activation, a pop-up dialog will appear, allowing you to specify the chains you’re interested in visualizing:
Benefits of Using the Sequence View
The synchronized interaction between the Sequence View and the 3D Viewport is a game-changer. For example:
- You can select residues in one view (Sequence View, Document View, or 3D Viewport), and the selection will automatically reflect in all views.
- The colorization feature allows you to color residues based on biophysical properties, ensuring critical properties of your structure are visually distinct. These colorations automatically propagate to the 3D Viewport, simplifying complex molecular analysis.
Streamline Your Molecular Modeling Workflow
By integrating the Sequence View into your modeling routine, you can save considerable time and reduce errors during molecular selection, coloring, and structural analysis. Whether you’re handling single chains or complex models with multiple chains, this tool ensures you maintain complete control and accuracy throughout the process.
Discover more about the Sequence View and its features in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.