For molecular modelers, navigating and interacting with complex molecular structures can often be a challenge. Connecting what’s happening in a sequence, a structure model, and the 3D viewport is not always seamless. The Sequence View feature in SAMSON addresses this difficulty by offering an interactive way to synchronize your molecular sequences with what you see in both the Document View and the 3D Viewport. This ensures selected residues remain in sync across visualizations, making your workflow significantly smoother.
What Makes Sequence View Useful?
The Sequence View is not just a convenience—it can be a productivity enhancer for anyone working with large molecular systems:
- Selection Sync: Residues you select in the Sequence View get automatically selected in the 3D Viewport and the Document View. Similarly, selecting residues in other views updates the Sequence View dynamically, ensuring complete synchronization across your workflow.
- Residue Coloring: The Sequence View allows you to colorize residues based on their biophysical properties. These colors can then be transferred directly to the structures in the 3D viewport for enhanced visualization and presentation.
- Choice for Multi-chain Structures: If your molecular model contains multiple chains, Sequence View provides you with the flexibility to choose which chain or chains you want to inspect and manipulate.
Accessing the Sequence View
The Sequence View is simple to activate, depending on the context of your workflow:
- Via the Home Menu: Navigate to the Home menu and click on the View sequence command. This option ensures quick access to the Sequence View at any point during your molecular modeling session.
- Via the Context Menu: Alternatively, you can right-click on a molecular structure in the workspace and select Structural model > View sequence. This method is useful if you’re directly working on a specific structure and prefer to open the Sequence View contextually.
If the structure you are analyzing contains multiple chains, a convenient dialog will prompt you to select the chains you want to visualize, making it easier to focus on specific portions of your molecular system:
By incorporating this feature into your workflow, you streamline the process of navigating complex molecular structures, visualizing relevant information, and making informed decisions based on the context of your sequences.
Visualizing with Enhanced Colorization
The Sequence View’s ability to colorize residues based on properties such as biophysical characteristics is a powerful tool for molecular modelers seeking clearer representations of their structures. You can use this function to emphasize specific properties like hydrophobicity or polarity and apply these color codes directly to the 3D Viewport. This not only makes the visualization aesthetically pleasing but also scientifically meaningful.
Curious to explore the full potential of the Sequence View? Check out the detailed documentation page here: https://documentation.samson-connect.net/users/latest/sequence-view/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.