When working with molecular systems, the way data is visualized often makes a huge difference in understanding structure and function. A common challenge among molecular modelers is navigating the visual complexity of nanosystems without getting overwhelmed or missing crucial insights. That’s where visual models in SAMSON come in.
Visual models provide graphical representations of molecular structures and fields, helping users interpret results, present data clearly, and even select atoms through surfaces based on specific visualization styles. Let’s dive into the different use cases and possibilities offered by visual models in SAMSON.
What is a Visual Model?
A visual model in SAMSON is a graphical representation applied to nodes in a document. Examples include:
- Secondary structure views of proteins
- Gaussian or solvent-excluded surfaces
- Volumetric representations of fields (e.g., electrostatic potential)
- Isosurfaces of scalar fields such as electron density
These models help transform raw atomic data into interpretable forms, offering clarity without altering the underlying system.
Adding and Using Visual Models
There are a few ways you can apply visual models in SAMSON:
- Using the context toolbar menu when a node is selected
- Via the menu: Visualization > Add > Visual model
- Keyboard shortcut:
Ctrl/Cmd + Shift + V
Once added, visual models can help you to see structure more clearly or highlight specific features depending on your task.
For example, if you’re analyzing a protein’s surface morphology, a solvent-excluded surface or an electrostatic field representation gives you intuitive insight into molecular interactions that may not be apparent from a stick or ball-and-stick model.
Customizing Visual Models
You can fine-tune the parameters of a visual model directly within the Inspector. First, select the visual model in the Document view, then click Inspect in the context menu.
Parameters might include surface thresholds, coloring schemes, or transparency, depending on the model used. This level of customization allows for better presentation and deeper analysis.
Visual Models as Interaction Tools
In SAMSON, visual models go beyond passive rendering. For instance, you can use the visible surfaces to select atoms, residues, or chains directly — especially useful with selection filters. This bridges visual representation and structural manipulation efficiently.
Extending Your Toolkit
If the default visual models don’t cover your needs, you can expand your set via SAMSON Connect or start developing your own using the extension generator. Open access to additional visualization styles allows the platform to grow with your research needs.
To learn more about visual models in SAMSON, 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 download SAMSON at https://www.samson-connect.net.