For structural biologists and molecular modelers, the frustration of navigating complex macromolecular systems is all too familiar. You often know the residue or chain you need to focus on—but shifting through a crowded 3D visualization can be tedious and inefficient. This is where the Sequence View in SAMSON comes in.
The Sequence View offers a clear, linear representation of molecular structures, making it easier to select, inspect, and modify proteins, DNA, RNA, and other polymers. But it does more than just display residues; it creates a bridge between sequence data and 3D visualizations, offering a level of control that can significantly speed up your modeling process.
What Is the Sequence View?
The Sequence View in SAMSON displays the polymer chains of selected molecules as a sequence of residues or nucleotides. Each residue is clickable and interactively linked to the 3D view. Need to locate a specific amino acid in chain B of your protein? Click it in the Sequence View, and it’s immediately highlighted in the 3D structure.
This one-to-one mapping between sequence and structure helps reduce trial-and-error operations and helps with editing complex systems, preparing simulations, or inspecting binding sites.
Why Use It?
- Easy access to residues: No more rotating endlessly in 3D space. Select a residue directly from the sequence list.
- Multi-residue selection: Shift-click or Ctrl-click to select an entire motif, domain, or functional region.
- Functional annotation aid: Use the sequence to keep track of active sites or modification points.
- Streamlined editing: Select a sequence region and quickly apply color schemes, visibility settings, or launch further analysis.
Common Use Cases
1. Binding pocket identification: Highlight active residues in the sequence pane and isolate them in the 3D view for docking studies.
2. Mutation design: Locate a mutation site in the sequence and easily modify the residue if you’re designing variants or running stability analysis.
3. Viewing non-standard residues: The Sequence View doesn’t hide residues that other tools might, like PTMs (post-translational modifications). Everything is listed clearly.
For modelers working with large systems, this is not just a visualization tool—it’s a productivity booster.
Tips for Effective Use
- Use the Sequence View in combination with SAMSON’s Visual Presets for quick style changes of selected residues.
- Turn on color coding to distinguish different chains or molecular features easily.
- Use the Sequence View alongside the Interaction Designer to study local interactions or prepare targeted simulations.
The Sequence View simplifies tasks that previously involved multiple selection steps and viewport adjustments. It helps modelers stay focused, reduces errors, and supports faster hypothesis testing.
To explore more features and customization options of the Sequence View, and how it integrates with the broader SAMSON platform, visit the official documentation page: https://documentation.samson-connect.net/users/latest/references/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.