Molecular modeling often involves interpreting complex nanosystems. One frequent challenge for molecular modelers is visualizing intricate structures and data in an accessible way. That’s where visual models in SAMSON, the integrative molecular design platform, come in handy. Visual models provide powerful graphical representations to make nanosystem exploration more intuitive and efficient.
What are Visual Models?
Visual models in SAMSON create graphical representations of nanosystems to enable a deeper understanding of the structures and fields you are working with. These representations include secondary structure depictions of proteins, Gaussian surfaces, isosurfaces of electron densities, volumetric representations of electrostatic fields, and more.
With SAMSON, you get a set of default visual models. Beyond that, you can easily expand your toolkit by downloading additional visual models from SAMSON Connect or by developing custom extensions using the platform’s extension generator (learn more here).
How to Apply Visual Models?
Applying visual models in SAMSON is both easy and flexible. You can apply them to a specific selection of nodes (atoms, residues, molecules, etc.) or extend the visualization to the entire nanosystem. Here are some ways to get started:
- Use the context toolbar menu specific to your selection.
- Navigate to Visualization > Add > Visual model.
- Apply a shortcut: press Ctrl/Cmd + Shift + V.
Adjust Visual Model Parameters
For some visual models, SAMSON enables further customization via the Inspector. For instance, when selecting a structural model visualized using a secondary structure representation, simply click on Inspect in the context menu. You’ll find visualization parameters that you can modify to suit your specific needs.
Here’s a look at what detailed customization could look like:
Highlight and Select Elements Directly
SAMSON’s default visual models come with an exciting feature: the ability to directly highlight and select elements such as atoms, residues, and chains via the rendered surfaces. This highly interactive experience is influenced by the current selection filter you have applied. For example, if you are working with a solvent-excluded surface, you can efficiently interact with specific residues right through the visualization.
Need to Create Your Own Visual Models?
While the default set of visual models is extensive, researchers with more specific needs can create their own. SAMSON offers detailed guidelines for generating new extensions, enabling you to design visual models that cater to niche applications in molecular modeling. Start with the extension generator documentation.
For more details about visual models and their applications in molecular modeling, visit the original documentation page: https://documentation.samson-connect.net/users/latest/models/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.