Making Molecular Systems Visually Intuitive with Visual Models in SAMSON

For molecular modelers, translating complex nanosystems into meaningful graphic representations is a recurring challenge. This is where SAMSON’s visual models come into play, offering comprehensive and customizable tools to bridge the gap between complex data and understandable visuals. Whether you’re analyzing protein structures or studying fields like electron density, visual models provide powerful visualization options with minimal effort.

What are Visual Models in SAMSON?

Visual models are graphical representations designed to bring nanosystems to life. These include structural visualizations like secondary structures of proteins, surfaces such as electron densities, or even volumetric representations of electrostatic fields. Such tools empower researchers to analyze and interpret intricate nanosystems effortlessly.

By default, SAMSON provides a set of ready-to-use visual models, and additional ones can be obtained from SAMSON Connect. There’s also room for developers to extend the functionality by creating custom visual models (learn how).

Getting Started: Applying Visual Models

Applying visual models in SAMSON is simple and efficient. You can apply them to selected nodes or the entire document, depending on your needs. Here’s how:

  • Context Toolbar: Use the context toolbar menu to swiftly apply a visual model to a selection.
  • Menu Navigation: Go to Visualization > Add > Visual model to explore and select the desired visual representation.
  • Keyboard Shortcut: For quicker execution, use Ctrl/Cmd + Shift + V to add visual models directly.

Customizing Your Visual Models

Sometimes a default visualization might not perfectly suit your needs. Luckily, several visual models have customizable parameters that can be adjusted via the Inspector tool. To tweak these parameters:

  • Select the visual model in the Document view.
  • Click on the Inspect option in the context menu to access its visualization settings.

Secondary structure visual model parameters in the Inspector

Tasks like highlighting specific atoms, residues, or chains within a nanosystem can also be executed efficiently. For instance, SAMSON enables selections via surfaces using the selection filter.

Highlighting residues on the Solvent Excluded Surface

Visual Examples

The versatility of SAMSON’s default visual models means you’ll find representations that suit almost every need. Here’s an example of some built-in models:

Some default visual models

Taking It a Step Further

What if the existing visual models aren’t enough? SAMSON provides a platform for developers to create customized visual models. If you’re interested in diving deeper into development, check out the Extension Generator or explore the Documentation center for detailed guidance on writing new models. Whether you’re focusing on protein dynamics, molecular interactions, or energy visualizations, SAMSON offers the flexibility you need to tailor visualizations to your requirements.

Learn More

With SAMSON, transforming molecular data into interpretable graphics is more accessible than ever. Explore more about visual models and their applications directly in the SAMSON documentation at https://documentation.samson-connect.net/users/latest/models/#visual-models.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get started by downloading SAMSON from https://www.samson-connect.net.

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