For molecular modelers, effectively visualizing nanosystems plays a pivotal role in understanding structural dynamics and functionalities. SAMSON offers a robust solution with its Visual Models. By providing graphical representations of nanosystems, visual models allow users to explore data intuitively while enhancing the clarity of what they are analyzing.
What Are Visual Models?
Visual models are tools in SAMSON that graphically represent aspects of your nanosystem. For example, they can depict protein secondary structures, gaussian surfaces, the isosurfaces of electron densities, volumetric electrostatic fields, and more. They work seamlessly with other SAMSON tools to deliver a comprehensive modeling experience.
Why Are They Useful for Molecular Modelers?
Understanding molecular structures at various levels of detail is a common challenge. Whether you’re working with structural data, fields, or specific molecular properties, visual models help you visually interpret your nanosystem. Highlighting and selecting parts of molecules, such as atoms, residues, or chains, becomes easier when these are coupled with the system’s surfaces and selection filters. The result? Streamlined workflows and more efficient modeling processes.
Available Visual Models in SAMSON
SAMSON comes pre-equipped with a variety of visual models. If the built-in options aren’t enough, SAMSON Connect lets you explore and add more models via SAMSON Extensions. Here’s a visual showing some default visual models in action:
How to Use Visual Models
Applying a visual model to your nanosystems in SAMSON can be done in several ways:
- Using the context toolbar menu of a selection.
- Via the Visualization > Add > Visual model menu option.
- Using the shortcut: Ctrl/Cmd + Shift+V.
Once applied, many visual models also provide ways to fine-tune their parameters. For example, you can adjust visualization settings directly through the Inspector. To modify a visual model:
- Select the model in the Document view.
- Click Inspect in the context menu to open its parameters.
Below, you can see an example of adjusting parameters for the Secondary Structure visual model:
Customizing Your Visual Models
If you want to develop your own visual models for unique needs or advanced simulations, SAMSON’s Extension Generator is a great place to start. Detailed documentation will guide you on creating new models and expanding SAMSON’s capabilities to suit your molecular modeling challenges.
Benefits of Using Visual Models
Visual models simplify molecular analysis, making it easier to select and highlight specific molecular features dynamically. For example, using a Solvent Excluded Surface allows residues or chains to be visually distinguishable, facilitating quick selections as shown below:
With visual models, intuitive molecular exploration becomes accessible to both new and experienced modelers, fostering better research outcomes.
To explore these features and more, visit the original documentation page at https://documentation.samson-connect.net/users/latest/models/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON from SAMSON Connect.