Molecular modelers often face the challenge of effectively visualizing nanosystems. Whether working on proteins, electron densities, or electrostatic fields, robust visual representations are crucial for both interpretation and communication. SAMSON offers practical tools to make this process seamless through its Visual Models. Let’s explore how you can simplify and enhance molecular visualization using SAMSON’s built-in features.
What Are Visual Models?
Visual models in SAMSON are designed to provide graphical representations of nanosystems. They include representations such as secondary structures of proteins, Gaussian surfaces, isosurfaces of electron densities, and volumetric depictions of electrostatic fields. These visualizations enable users to better understand structures and properties of their systems.
Using Visual Models
Adding visual models to your projects in SAMSON is straightforward. To apply a visual model:
- Use the context toolbar menu for the selected nodes.
- Go to Visualization > Add > Visual model.
- Use the shortcut: Ctrl/Cmd + Shift+V.
If no nodes are selected, the visual model applies to the entire document. To dive deeper, refer to SAMSON’s Visualizing guide.
Customizing Visualization Parameters
Many visual models in SAMSON allow you to tweak visualization settings. For example, you can adjust parameters for a secondary structure model in the Inspector. Simply select the visual model in the Document View and click on Inspect in the context menu. This enables you to precisely control how your structures or fields appear, tailoring them to your specific research needs.
Interactive Highlighting and Selection
SAMSON’s default visual models let you interactively highlight and select entities such as atoms, residues, and chains. For example, on a solvent-excluded surface visualization, you can use selection filters to perform specific tasks with ease. This streamlines your analysis and increases productivity dramatically. See the example below of highlighting residues:
Extending Visual Models
Beyond the default models, SAMSON users can incorporate new visual models from SAMSON Connect. For advanced users or developers, SAMSON offers the opportunity to build custom visual models using its extensibility framework. To learn more about creating your own extensions, visit the Extension Generator page.
Visual models are a powerful feature of SAMSON that help molecular modelers streamline their workflow and enhance their understanding of nanosystems. To explore these functionalities further, visit the original documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use.