One of the frequent challenges faced by molecular modelers is efficiently working with specific residues in a complex biomolecular structure. How do you easily highlight, work on, and visualize selected residues across multiple views for downstream molecular workflows? Enter SAMSON’s Sequence View, a powerful and interactive feature designed to simplify residue selection and improve your molecular modeling efficiency.
What is the Sequence View?
The Sequence View in SAMSON is an interactive tool that provides a synchronized molecular sequence representation. This synchronization links the Sequence View with the Document View and the 3D Viewport: residues selected in one view automatically get selected in the other views. For instance, selecting residues in a structure in 3D is immediately reflected in the sequence, and vice versa. This bi-directional interaction eliminates redundancy and helps streamline workflows dramatically.
Key Features of the Sequence View
1. Direct Interaction with the Sequence: In the Sequence View, you can click on residues directly within the presented sequence. Whether it’s selecting specific amino acids for analysis or isolating segments for editing, this interaction reduces the time spent navigating large structures.
2. Colorize Based on Biophysical Properties: The Sequence View lets you apply color schemes to residues based on their biophysical properties, such as polarity or hydrophobicity. These colorizations can enhance visual clarity across complex structures and are automatically reflected in the 3D Viewport for consistency.
Color coding provides a quick way to interpret structural data and communicate findings effectively to collaborators.
Accessing the Sequence View
Accessing the Sequence View in SAMSON is straightforward. Choose what works best for your workflow:
- From the Home Menu: Click the View sequence command under the Home menu.
- From the Context Menu: Right-click on a structure, then select Structural model > View sequence in the context menu.
If a structure contains multiple chains, a convenient pop-up lets you select which chain(s) to display in the Sequence View.
Why Use the Sequence View?
The Sequence View is not just an organizational aid—it is a productivity booster. It helps modelers:
- Quickly identify and select residues for downstream workflows.
- Easily apply biophysical coloring to improve structural insights.
- Ensure synchronization between molecular sequence and structure representations.
Whether you’re preparing a structural model for publication or focusing on specific interactions in protein engineering, the Sequence View is a critical tool for saving time and simplifying your work.
Learn More
If you’re eager to utilize the Sequence View to elevate your molecular modeling workflows, make sure to check out the official Sequence View documentation.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.