One of the common challenges in molecular modeling — whether you’re analyzing proteins, designing nanosystems, or preparing presentations — is clearly communicating what you’re seeing. At the atomic and molecular scale, raw geometry and topology data can quickly become hard to interpret. This is where Visual Models in SAMSON can help.
Visual models are tools that allow molecular modelers to control how molecules and nanosystems are displayed graphically. They don’t just make visuals prettier — they help make sense of complex systems by turning data into accessible and intuitive representations.
Why Visual Models Matter
Imagine you’re exploring a protein and want to highlight its secondary structure, or visualize the spatial distribution of an electron density. Without a proper visual model, this information might remain hidden in a cloud of atoms and bonds. A visual model lets you reveal what matters and suppress the noise.
By changing how your data is displayed, you make it easier to analyze, communicate, and understand. This becomes especially useful when collaborating with others or preparing for publications and presentations.
Types of Visual Models in SAMSON
SAMSON provides a variety of visual models by default. These include:
- Secondary structure representation — to quickly visualize helices and sheets in proteins
- Gaussian surfaces — to represent molecular orbitals
- Electron density isosurfaces — useful for crystallographic data
- Electrostatic field representations — using volumetric or vector field visuals
You can apply visual models to a specific selection (like atoms or residues), or to the whole system. The easiest way is through the context menu or by using the keyboard shortcut: Ctrl/Cmd + Shift + V.
Customizing Visual Models
Once a visual model is applied, you can explore its parameters using the Inspector. You can fine-tune style, transparency, color schemes, and more. For example, if you’ve applied a Secondary Structure model to a protein, you can adjust how different coils and helices are rendered, offering more visual clarity or alignment with your preferences.
Interacting with Visual Models
Visual representations aren’t just static images — they can be interactive. If you use a Solvent Excluded Surface, for example, you can pick atoms or residues visually, which is especially helpful during model editing or analysis.
Getting More Visual Models
If the default options are not enough, more visual model types can be added from SAMSON Connect. And if you’re into development, you can also create your own through SAMSON Extensions — useful for setting up visuals specific to your research needs.
Conclusion
Whether you’re analyzing complex molecular systems or sharing your work with others, visual models in SAMSON allow you to present your models more clearly and effectively. They are not just cosmetics — they are a practical bridge between raw data and human understanding.
To explore more ways to use visual models, visit the official documentation at https://documentation.samson-connect.net/users/latest/models/.
Please note that SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.