Molecular modelers often face the challenge of analyzing complex molecular structures and making sense of detailed sequence information across different visualization modes. Keeping molecular sequences, 3D structures, and document views in sync is a frequent pain point — especially when identifying residues of interest or applying property-based modifications to visualize models effectively.
SAMSON’s Sequence View offers a clean and interactive solution to this problem by connecting molecular sequence data with 3D visualizations and document views in real time. Here’s how this feature can make your workflow much smoother:
Interactive Synchronization with Sequence View
When using Sequence View in SAMSON, you no longer need to jump between disconnected tools or workspaces. This tool functions as a dynamic bridge between molecular sequence data and your 3D Viewport:
- Select residues in the Sequence View, and they are automatically selected in the Document View and the 3D Viewport.
- Similarly, residues selected in the 3D Viewport reflect instantly in the Sequence View for seamless synchronization.
Colorize and Visualize Based on Biophysical Properties
One major benefit of the Sequence View tool is its ability to help visualize molecular sequences in new ways. You can colorize residues based on biophysical properties like polarity, charge, or hydrophobicity. Once colorized, you can transfer these custom color schemes directly to the 3D Viewport, enabling you to:
- Enhance the clarity of the molecular interactions you’re working on.
- Improve the visual representation of the molecular structure in presentations or collaborative sessions.
Multiple Access Points for Flexibility
Want to pop into Sequence View quickly? SAMSON gives you not one but two different ways to access it easily:
- From the Home menu:
Choose the View sequence command, located in the Home menu, and instantly dive into this feature. - Via the Context menu:
Right-click on a structure in the Document View or 3D Viewport, and select Structural model > View sequence to pull up the Sequence View.
Customizing Chains for Complex Structures
If you’re working with a molecular structure that contains multiple chains, SAMSON ensures that the Sequence View is adaptable. When you access the tool, a dialog box will appear to let you choose specific chains to view. Whether you are focusing on a single chain or multiple chains at the same time, this pop-up makes it easy to keep everything relevant to your immediate tasks.
Conclusion
SAMSON’s Sequence View streamlines your integrative molecular modeling workflow by synchronizing molecular sequence data with 3D visualization and adding valuable customizations with colorization tools. Whether you’re preparing for a research presentation or diving into structural design details, Sequence View can be your go-to feature. Start using it today to simplify your molecular modeling process!
To dive deeper into SAMSON’s Sequence View capabilities, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.