When visualizing complex molecular systems, clarity matters. Whether you’re highlighting interactions within a protein pocket or exploring electron density fields, effective visuals can save time, avoid misinterpretations, and enhance presentations or publications. But creating meaningful visuals from raw structural data can be time-consuming, especially when default settings aren’t enough.
This is where SAMSON Extensions — and particularly visual models — can help. Without writing code, molecular modelers can use SAMSON’s modular system to tailor how their systems are shown, from surfaces and secondary structures to field isosurfaces.
What are visual models?
In SAMSON, visual models are a type of extension designed to visually represent data in the viewport. These models are not limited to atoms and bonds; they can depict abstract properties like electrostatics, surface curvature, or secondary structure motifs.
Examples include:
- Secondary structure ribbons for proteins
- Electron density isosurfaces
- Volume renderings of scalar fields
These views help better understand molecular environments and interactions, and are especially useful in domains like structure-based drug design or materials analysis.
How do I use visual models?
When you first launch SAMSON, it downloads a default set of SAMSON Extensions, including basic visual models. You can start using them immediately from the left-side menu in the viewport or by searching in the top bar (“Find everything” search box).
But SAMSON’s real strength lies in its flexibility. You can extend your visual tools with more visual model extensions from the SAMSON Connect Marketplace. This lets you bring in domain-specific tools — for example, visualizations tailored for nucleic acid topologies or advanced electron density mapping tools.
Why use visual models instead of static renderings?
If you’re used to exporting structures into third-party visualization tools, you’ve likely run into workflow breaks: reexporting, reintegrating changes, and manually adjusting representations. With SAMSON’s visual models, the representations update live as your data changes, and they are integrated into your modeling workflow. That means you can, for instance, simulate conformational dynamics and immediately see state-dependent changes in the visualization.
More advanced users can even develop new visual models themselves using the SAMSON SDK, but this post focuses on visual exploration without development.
Getting started
To try out visual models:
- Download SAMSON (free for non-commercial use).
- Search for an extension (e.g., “Isosurface Viewer”) in the SAMSON Connect Marketplace.
- Install the extension and open any molecular system.
- Use the visual model from the left-side menu of the viewport.
Once added, you can adjust representations dynamically — change isovalue thresholds, modify surfaces, or switch between ribbon and tube representations. You’ll instantly see how these views help communicate molecular properties more effectively.
To learn more about how to enhance your work with visual models and other SAMSON Extensions, visit the official documentation page: Extending SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, visit https://www.samson-connect.net.