Visualizing molecular systems effectively is one of the key challenges faced by scientists, researchers, and educators working in structural biology, drug design, and materials science. Molecules are complex, and meaningful insights often depend on being able to visualize relevant structures and properties clearly, especially in large systems. If you’ve struggled with interpreting raw data files, deciphering coordinate sets, or navigating abstract force fields, you’re not alone.
In SAMSON, visual models provide a bridge between data and understanding. They enable users to choose how different aspects of a system are displayed, highlight key features, and explore relationships between regions or properties of a molecule. Let’s dive into how visual models in SAMSON help solve the pain of “seeing” your nanosystem.
What Exactly Are Visual Models?
Visual models in SAMSON are used to graphically represent structural or computed information. These may range from conventional representations like ribbons and ball-and-stick to more advanced renderings such as Gaussian surfaces, isosurfaces of electron density, or volumetric representations of electrostatic fields.
They are not just for aesthetics—visual models help focus your analysis on specific parts of a system, like active sites, surfaces, or channels. They accelerate understanding, facilitate communication, and improve presentations—even your own internal comprehension of a simulation.
How to Apply Visual Models
Here are several easy ways SAMSON allows you to apply visual models:
- Right-click on your selection and choose from the context toolbar.
- Use the menu: Visualization > Add > Visual model.
- Keyboard shortcut:
Ctrl (or Cmd) + Shift + V
When nothing is selected, visual models are applied to the entire scene by default. But they can also be finely tuned to specific nodes—like an individual chain or residue—based on your selection filter. That way, you can focus just on what matters.
Examples of Default Visual Models
Here’s how SAMSON displays molecules using built-in visual models:
Customizing Visual Models
Some visual models have configurable parameters you’d want to adjust depending on your case. To tweak them:
- Open the Document view, and select the visual model.
- Right-click and choose Inspect.
- Modify parameters, such as segmentation granularity, color scale, and surface transparency in the Inspector.
This level of customization enables better presentations and clarity when sharing your findings with others or preparing presentations.
Highlighting Features with Selection Filters
Depending on the current selection filter, you can directly click on surfaces to select atoms, residues, or chains. This is particularly useful when using representations like Solvent Excluded Surfaces:
Extending Your Toolkit
SAMSON provides a set of visual models by default, but you’re not limited to those. You can download more from SAMSON Connect, or even develop your own using the Extension Generator.
Conclusion
Effective visualization transforms raw molecular data sets into tangible scientific insights. Whether you’re a beginner trying to navigate protein structures or an experienced modeler preparing figures for publication, SAMSON’s visual models offer intuitive methods to explore and communicate complex molecular systems.
Learn more from the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started at samson-connect.net.