One of the most common challenges in molecular modeling is making sense of complex molecular systems. Beyond raw data like atom coordinates, researchers need intuitive visual representations to explore, analyze, and communicate their findings effectively.
This is where visual models in SAMSON come in. They transform raw molecular data into understandable shapes, surfaces, and fields — crucial for insight-driven modeling workflows.
What are Visual Models?
Visual models in SAMSON are graphical representations that can be applied to structures in your document. Think of them as different ‘masks’ you can apply to the same system to see distinct features: secondary structures, molecular surfaces, electrostatic fields, and more.
Some examples include:
- Secondary structure representations for proteins (e.g., alpha-helices, beta-sheets)
- Gaussian surfaces and solvent-excluded surfaces
- Volumetric maps like electron density or electrostatic potential
How to Apply Visual Models
Visual models can be applied in several intuitive ways:
- Through the context toolbar after selecting atoms or molecules
- From the top menu via Visualization > Add > Visual model
- Using keyboard shortcuts: Ctrl / Cmd + Shift + V
These allow users to quickly switch between views and highlight different parts of a structure depending on what they’re investigating.
Customizing Visual Models
Once applied, many visual models offer real-time control over their appearance. You can select a visual model in the Document view, right-click, and choose Inspect to open the Inspector. Here you can adjust visualization parameters to tailor the model’s look and behavior to your needs.
Highlight selections are made easy as well. For instance, when a solvent-excluded surface is shown, SAMSON allows direct selection of residues through the surface interface, depending on your selection filters.
Adding or Developing Your Own
SAMSON includes a set of default visual models, but you can also add more from SAMSON Connect or build your own using the Extension Generator.
This makes the platform adaptable for specific scientific needs, whether you work with nucleic acids, protein complexes, or custom datasets like membrane systems or nanotubes.
Why This Matters
Effective visual representations are often what make the difference between struggling with interpretation and discovering insights. Whether you’re understanding protein folding pathways, bonding interactions, or electrostatic environments, visual models simplify the process and let you focus on your science.
To learn more, visit the full documentation on SAMSON Models.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at www.samson-connect.net.