When working with complex nanosystems, one of the biggest challenges scientists and engineers face is how to efficiently visualize and interact with molecular structures. It’s not just about seeing atoms and bonds — we need to understand higher-level organization, surface properties, electrostatic fields, and more. Thankfully, SAMSON offers a powerful set of visual models that make this much easier.
Why Visual Models Matter
Visualization isn’t just cosmetic — it can help you detect issues, validate hypotheses, and communicate results clearly. For example, viewing a protein’s secondary structure or mapping electrostatic potential over a molecular surface can reveal insights at a glance. In SAMSON, visual models are designed exactly for that purpose: to represent data graphically while tied to the structure and properties of your nanosystem.
Types of Visual Models
SAMSON comes with several default visual models, and you can extend this through SAMSON Connect. Here are some typical examples:
- Cartoon representations of proteins (for visualizing secondary structures)
- Electron density isosurfaces
- Volumetric visualizations of electrostatic fields
- Solvent-excluded surfaces showing accessible regions
This richness in representation allows you to match the visualization to the scientific question you’re asking.
Applying Visual Models
To add a visual model to your document in SAMSON, you have a few options:
- Use the context toolbar that appears when you’ve selected atoms or molecules
- Navigate via Visualization > Add > Visual model
- Use the shortcut: Ctrl (or Cmd on macOS) + Shift + V
Visual models can be applied either to specific selections or to the entire document when nothing is selected.
Customizing Visual Models
One of the most useful features is the ability to fine-tune the appearance of visual models in the Inspector.
For instance, if you’re working with a secondary structure visual model, you’d simply select it in the Document view, then right-click and choose Inspect. There, you can update colors, layers, transparency, and more.
Interacting with Surfaces
SAMSON’s default visual models go beyond passive visualization — they can also facilitate interaction. For example, with solvent-excluded surfaces (SES), you can directly select atoms, residues, or chains visually. What appears as just an image is fully linked to the underlying molecular data, and selection behavior depends on your current selection filter.
Developing Your Own Visual Models
If you’re comfortable coding, SAMSON’s architecture allows advanced users to create their own visual models via the SAMSON Extension Generator. This is especially useful for those working in custom fields or wanting specific rendering methods.
Conclusion
Visual models in SAMSON can make complex nanosystems more intuitive and accessible, improving both understanding and productivity. Whether you’re visualizing a protein fold or examining electrostatic fields, the ability to switch views and interact with representations offers a flexible approach to molecular modeling.
To explore all visual model features and examples, visit the original documentation here: https://documentation.samson-connect.net/users/latest/models/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.