One common struggle for molecular modelers is turning complex molecular data into clear, insightful visualization. Whether you’re analyzing a protein’s folding, looking at an electron density map, or comparing molecular surfaces, effective visual representation is often the first step toward understanding your nanosystem.
This is where Visual Models in SAMSON come in. Visual models help translate abstract molecular structures and fields into intuitive visuals that you can manipulate, inspect, and share.
What Are Visual Models?
Visual models in SAMSON are graphical representations of nanosystems. Instead of working with raw data or geometry, they let you view elements such as:
- Secondary structures of proteins
- Electron density isosurfaces
- Electrostatic fields
- Surface representations (Gaussian, Solvent Excluded, etc.)
Why They Matter
Visual insight is often the fastest route to understanding a molecular system. A well-chosen visual model can highlight patterns, anomalies, or relationships that would be hard to spot in table-based or purely atomic representations. It’s also the foundation for effective presentations and collaboration with colleagues who may not use SAMSON directly.
Ready-to-Use Visual Models
SAMSON provides several default visual models you can apply immediately. Here’s a snapshot of some available options:
How to Apply a Visual Model
Applying a visual model in SAMSON is straightforward:
- Select the nodes you want to visualize (e.g., atoms, residues, etc.)
- Use the context toolbar menu or the application menu: Visualization > Add > Visual model
- Keyboard shortcut:
Ctrl/Cmd+Shift+V
If nothing is selected, the visual model is applied to the entire document.
Tailoring Visualization Settings
Some visual models allow parameters to be customized using the Inspector tool. Just select the visual model in the Document view and click Inspect from the context menu. This makes it easier to adjust coloring, resolution, or other appearance properties.
Advanced Selection with Visual Models
One particularly useful feature is the ability to select atoms, residues, or chains directly from their surface representations. This depends on the current selection filter you’re using.
Extending with Custom Visual Models
If you have specific needs or would like to create your own custom visual styles, SAMSON supports extensibility through its Extension Generator. This allows more control over what and how you visualize complex data in your nanosystem.
To explore the full capabilities of visual models in SAMSON, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.