One of the most common challenges in molecular modeling is effectively communicating complex molecular structures and interactions. Whether you’re collaborating with a cross-disciplinary team, preparing a presentation, or simply trying to understand your own simulation results, clear and customizable visualizations can make all the difference.
SAMSON provides a powerful way to approach this challenge, through visual models. These are separate from the structural information itself, and serve to enhance how molecular systems are represented on screen — improving clarity without altering the underlying data.
What are Visual Models?
In SAMSON, visual models give you graphical representations of nanosystems. Instead of manually going through rendering settings, you can use predefined visual models to quickly depict secondary structures, surfaces, fields, and more. For example:
- Secondary structure ribbons for proteins
- Gaussian and solvent-excluded surfaces for molecular boundaries
- Field isosurfaces for electrostatics and other properties
Why It Matters: Decoupling Visualization from Data
One key feature of visual models in SAMSON is that they are non-intrusive. They do not change the atomic coordinates or molecular structure — they simply change how things appear. This makes it safe and convenient to toggle different views depending on your needs without affecting your simulations or analysis.
Working with Visual Models
You can quickly apply visual models in several ways:
- Right-click on selected entities and use the context toolbar
- Use the menu:
Visualization > Add > Visual model - Keyboard shortcut: Ctrl/Cmd + Shift + V
If you do not select specific atoms or molecules, the model will be applied to the entire document.
Customizing Visual Output
Once a visual model has been applied, you can fine-tune the way it looks using the Inspector. For instance, if you’re using a secondary structure visual model, parameters like ribbon thickness and color scheme can be adjusted there.
This flexibility allows researchers to highlight specific regions, generate figures for publication, or illustrate different aspects of their systems more effectively. In addition, some visual models support interaction. For example, surfaces can serve as a visual basis for selecting residues or atoms — enhancing both communication and interactivity.
Extend with Custom Visual Models
SAMSON also supports the development of your own visual models through its Extension system. If the built-in options don’t cover your needs, or you want specific renderings tailored to your work, writing a custom visual model can be a valuable step. Learn more about building Extensions through the Extension Generator.
Whether you’re preparing figures for a publication or trying to explore the structure-function relationship in a molecule, SAMSON’s visual models offer non-disruptive, flexible ways to see more — and understand better.
To learn more about models in SAMSON, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.