One challenge that often arises in molecular modeling is how to effectively visualize complex nanosystems. Whether it’s a protein with hundreds of residues, or a molecular assembly involving several interacting species, understanding structure, function, and interactions becomes far easier when we can see them clearly.
This is where visual models in SAMSON can make a significant impact. Visual models are dedicated components that render graphical representations of nanosystems, making it easier to interpret information by mapping data to forms you can quickly grasp.
What Visual Models Are
Visual models in SAMSON are not just decorations—they help reveal essential spatial and structural insights, illustrate properties like electrostatic potential, and let users highlight specific molecules, residues, or atoms. They include representations such as:
- Secondary structure diagrams of proteins
- Gaussian surfaces
- Isosurfaces for scalar fields (e.g., electron density)
- Volumetric maps of properties like electrostatics
Getting Started with Visual Models
SAMSON ships with a default set of visual models you can use immediately. Applying a model is straightforward. You can:
- Right-click the selection and use the context toolbar
- Navigate to Visualization > Add > Visual model
- Use the shortcut Ctrl/Cmd + Shift + V
Visual models adapt to your current selection—automatically highlighting atoms, chains, or entire molecular structures depending on chosen filters and views.
Customizing Your View
Some visual models offer configurable options through the Inspector. This allows you to fine-tune how elements are displayed—for example, changing ribbon thickness for secondary structures or altering isosurface transparency. You can open the Inspector by selecting the model in the document view and choosing Inspect from the context menu.
Interaction for Deeper Insight
One especially helpful visual model feature is the ability to highlight and select specific components—like residues or atoms—directly from visual surfaces. This is particularly useful when working with complex selections or when inspecting solvent-excluded surfaces, where traditional selection tools may fall short.
Extending What’s Available
If the built-in visual models aren’t enough for your workflow, SAMSON makes it possible to build your own using its Extension Generator. These custom visual models can be tailored to your specific research domain for more targeted visual insights.
To learn more about visual models and their usage, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.