As a molecular modeler, visualizing structures effectively is vital—not just for presentation purposes, but also for developing an intuitive understanding of complex nanosystems. Whether you’re analyzing protein folding, inspecting electrostatic fields, or preparing publication-quality visuals, selecting an appropriate visual model can make your work clearer and faster.
SAMSON offers several built-in visual models that allow you to represent structures at different levels and with different styles. This post takes a closer look and provides a practical guide to help you understand and choose visual models depending on your use case.
What Are Visual Models in SAMSON?
Visual models in SAMSON provide graphical representations of molecular data. They work like visual overlays on your nanosystem structure, without altering its data. You can apply them to selected nodes (atoms, molecules, residues, etc.) or to the entire document.
Examples of visual models include:
- Secondary structure representations of proteins (e.g., cartoon models for helices and sheets)
- Gaussian or solvent-excluded surfaces
- Isosurfaces of electron density maps
- Volumetric representations of electrostatic fields
How to Apply Visual Models
You can add visual models in several ways:
- Right-click on your selection and use the context menu
- From the top menu: Visualization > Add > Visual model
- Use the shortcut:
Ctrl/Cmd + Shift + V
SAMSON provides a set of default visual models, and more can be added via SAMSON Connect through specialized extensions.
Hands-On Example: Comparing Visual Models
Below is an image illustrating various default visual models applied to the same protein structure (PDB: 1YRF):
The image highlights how different visual models can emphasize different features—helix structures, molecular surfaces, electron density, and more. Choosing the right view depends on what aspect of the system you wish to explore or communicate.
Customizing Visual Models
Some visual models have configurable parameters located in the Inspector. For example, you can adjust the resolution, opacity, and color mapping of a surface or field representation.
This flexibility allows you to tailor your visualizations to specific needs—be it clarity in presentations or fine-tuned structural analysis.
Interactive Highlighting and Selection
One underrated feature is how SAMSON’s visual models can assist with selections. For example, visual surfaces allow you to highlight and select residues, chains or individual atoms directly through the rendered surface, using the current selection filter.
This can make operations like assigning charges, applying constraints, or setting up simulations much faster and more intuitive.
Developing Custom Visual Models
If the existing visual models aren’t enough, SAMSON allows you to develop your own using its Extension framework. Refer to the Extension generator documentation to get started.
To learn more about how visual models work in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/models/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net