One of the more persistent frustrations for molecular modelers is effectively visualizing nanosystems—whether it’s a protein, an electrostatic field, or a more complex molecular structure. A clear and flexible visual representation can make all the difference in understanding, communicating, and analyzing structures and properties.
SAMSON, an integrative platform for molecular design, addresses this challenge with a powerful tool: visual models. These aren’t just aesthetic tools; they provide critical ways to understand nanosystems at different levels of detail and abstraction. Yet, many users only scratch the surface of what visual models can do.
What Are Visual Models?
In SAMSON, visual models define how the nodes (like atoms, molecules, or fields) are graphically represented. They are separate from structural data—meaning you can visualize the same structure in many different ways based on your current needs or the data you want to highlight.
Examples of visual models include:
- Secondary structure diagrams of proteins
- Gaussian or solvent-excluded surfaces of molecules
- Isosurfaces of electron densities
- Volumetric representations of fields like electrostatics
This modular system lets you not just see your data—but interact with it in meaningful, context-dependent ways.
Applying Visual Models
You can apply visual models to selected nodes or the entire document. There are several ways to do this quickly:
- Via the context toolbar on a selection
- Using the menu path: Visualization > Add > Visual model
- Using shortcuts:
Ctrl/Cmd+Shift+V
Interactive Visualization
What makes SAMSON visual models especially useful is that they are interactive. For example, using the Solvent Excluded Surface model, you can click on areas of the surface and immediately see which residue, atom, or molecule it’s associated with—based on the current selection filter.
This interactivity blends visualization with selection, helping molecular modelers quickly isolate relevant areas of interest.
Customizing Visual Models
Visual models come with adjustable parameters. These can be accessed through the Inspector panel:
- Click the visual model in the Document view
- Select Inspect from the context menu
Here, you can customize things like coloring schemes, representation styles, or display thresholds, helping to fine-tune what’s shown and what’s hidden. This is particularly useful in simulations or when preparing publication-quality images.
Add More Visual Models (or Build Your Own)
SAMSON comes with a set of built-in visual models, but you’re not limited to the default library. You can:
- Download additional models from SAMSON Connect
- Develop your own using the SAMSON Extension Generator
For research groups or labs with specific needs, this flexibility can be a time saver and a powerful addition to custom pipelines.
To learn more, refer to the full documentation on Visual Models in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at samson-connect.net.