Molecular modelers often face the challenge of effectively visualizing nanosystems to understand their structure, analyze interactions, and present data to collaborators. SAMSON, the integrative molecular design platform, offers a powerful solution with visual models: graphical representations that provide insights into the geometry, structure, and properties of nanosystems.
What are Visual Models?
Visual models in SAMSON provide a variety of representations such as secondary structures of proteins, gaussian surfaces, isosurfaces for electron density, or volumetric representations of electrostatic fields. These models make it easier to comprehend molecular structures and dynamics by offering customizable graphical views.
SAMSON supports a set of visual models by default, and additional visual models can be integrated through its SAMSON Connect platform or custom-developed extensions. The image below showcases some of the default visual models that come with SAMSON:
How to Apply Visual Models in SAMSON
Applying visual models is straightforward. Visual models can be applied to selected nodes, or to the entire document if no specific nodes are selected. There are multiple ways to apply visual models:
- Via the context toolbar menu of the selection.
- Using the menu path: Visualization > Add > Visual model.
- By using the shortcut: Ctrl/Cmd + Shift+V.
For new users looking to understand the process better, the Visualizing section in the SAMSON documentation covers this task in detail.
Customizing Visual Model Parameters
Once a visual model has been applied, modelers can further customize its visualization parameters. These parameters can be found in the Inspector. To access them:
- Select the visual model in the Document view.
- Right-click and choose Inspect from the context menu.
The image below shows an example of modifying secondary structure parameters for a visual model:
Advanced Features
Visual models in SAMSON are highly interactive. For instance, they allow highlighting and selecting atoms, residues, chains, and more directly via surfaces, depending on the current selection filter. This feature is especially useful for tasks like focusing on specific regions of interest in a molecule or protein.
In addition, custom visual models can be developed to cater to specific needs. For those interested in extending SAMSON, detailed guides on generating SAMSON Extensions are available in the developer documentation.
Conclusion
Visual models are indispensable tools for molecular modelers aiming to better understand, analyze, and communicate molecular data. By leveraging these tools in SAMSON, you can visualize your nanosystems with clarity and precision while tailoring these representations to your exact needs. To explore the full potential of visual models, visit the official documentation: https://documentation.samson-connect.net/users/latest/models/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can access the platform by visiting https://www.samson-connect.net.