When modeling complex molecular systems, clarity matters. Whether you’re studying proteins, designing new molecules, or preparing figures for publication, being able to see your data in a meaningful and customizable way can dramatically improve your workflow.
This is where SAMSON’s visual models come into play. Instead of just rendering atoms and bonds, visual models in SAMSON offer a wide range of graphical representations that allow you to understand structure, function, and interactions more intuitively.
Why Use Visual Models?
One common challenge in molecular modeling is interpreting large or complex systems. Atomic representations can be dense, cluttered, and hard to interact with—especially when you’re handling proteins, supramolecular structures, or large reaction systems. Visual models solve this by enabling simplified, structured, and interactive graphics that emphasize what matters.
What Can You Do With SAMSON’s Visual Models?
SAMSON comes bundled with several ready-to-use visual models, including:
- Secondary structure representations for proteins
- Gaussian surfaces illustrating electron densities
- Isosurfaces for scalar fields
- Volumetric representations of electrostatic fields
Applying a visual model is simple and can be done via:
- Context toolbar on selected nodes
- Visualization > Add > Visual model
- Keyboard shortcut:
Ctrl/Cmd + Shift + V
Interactive Visualization
Once applied, visual models aren’t just static images. You can interact with them to select atoms, residues, or chains directly from the surface—depending on your selection filter. For example, highlighting residues on a solvent-excluded surface can help pinpoint areas of interest during surface analysis or interface exploration.
Customize What You See
Some visual models are configurable. You can tweak their appearance and behavior through the Inspector panel. Just select the model in the document view and choose Inspect from the context menu to access settings like transparency, color schemes, and threshold values.
Extending Visual Capabilities
Need a specialized visualization? You can always add new visual models from SAMSON Connect, or develop your own using the Extension Generator. This is especially useful for researchers working with new types of data or needing tailored visual representations.
To learn more about visual models in SAMSON and how to make the most of them, check out the full documentation at 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.