Graphical representation of molecular structures is a key aspect of molecular modeling. Whether you’re visualizing protein structures, analyzing electronic density, or inspecting electrostatic fields, having clear and detailed visuals makes a world of difference. In this blog post, we’ll dive into visual models in SAMSON, an integrative platform for designing and modeling nanosystems.
What Are Visual Models?
Visual models in SAMSON are used to provide graphical representations of nanosystems. For example, they can depict:
- The secondary structure of a protein
- Gaussian surfaces
- Electron density isosurfaces
- Electrostatic field volumetric representations
By default, SAMSON comes equipped with various visual models. Moreover, you can enhance your toolkit with additional ones available through SAMSON Connect or by creating custom-made models if you’re a developer.
Applying Visual Models
Applying visual models in SAMSON is straightforward. Here’s how you can bring your molecular data to life:
- Use the context toolbar menu to apply visual models to selected nodes (or the entire document if nothing is selected).
- Access the dropdown menu under Visualization > Add > Visual model for more options.
- Utilize the shortcut: Ctrl/Cmd + ShiftV.
To better understand the behavior of these visual models, SAMSON offers a visualizing tutorial, accessible here.
Fine-Tuning Visual Models
Some visual models allow you to adjust their parameters for better customization. You can do so through the Inspector tool. Follow these steps:
- Select the visual model in the Document view.
- Right-click and select Inspect from the context menu.
For example, if you’re working on a secondary structure model, you can stylize the representation to enhance clarity and focus on specific elements of your system. Below is a screenshot showcasing parameters being modified in the Inspector:
Interactive Features of Visual Models
SAMSON’s default visual models offer intuitive interactions. You can highlight and select residues, chains, atoms, and more, directly on surfaces. This is especially helpful when analyzing specific regions of interest. Selection features will vary depending on your current selection filter.
An example of highlighting residues on a Solvent Excluded Surface is shown below:
Customize Your Visual Models
If you’re experienced with programming, SAMSON provides tools and documentation to help you develop your own visual models. Building a tailored visual model for your molecular systems can significantly improve the way you interact with complex data.
Want to learn more? Visit the documentation page on visual models to explore this feature further and uncover what SAMSON can do for your molecular modeling journey.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON for free at SAMSON Connect.