When starting out with molecular modeling in SAMSON, one of the first challenges you may encounter is how to make your molecular structures both informative and visually clear. Whether you’re preparing a figure for a publication or trying to make sense of a complicated molecular interface, visualizing the right parts of your nanosystem can save hours of work.
This is where Visual Models come in. In SAMSON, visual models aren’t just decorative. They’re tools to help you explore, analyze, and communicate your data more effectively.
What Are Visual Models in SAMSON?
Visual models in SAMSON serve one main purpose: to provide graphical representations of your nanosystems. These include a variety of visualization methods, such as:
- Secondary structure representations (especially useful for proteins)
- Gaussian and isosurfaces (useful for visualizing electron densities)
- Volumetric fields like electrostatic maps
- Solvent-excluded surfaces that allow for intuitive selection and highlighting
Applying Visual Models Efficiently
There are several ways to apply visual models in SAMSON:
- Use the context toolbar that appears when you select atoms or molecules
- Navigate via Visualization > Add > Visual model
- Use the shortcut: Ctrl/Cmd + Shift + V
These methods ensure you can quickly apply the appropriate visual model to either selected nodes or to the entire system—depending on your needs.
Adjusting Parameters for Better Insights
Many visual models come with adjustable parameters. You can tweak these to highlight the information that matters most to you. For instance, in the Inspector, selecting a visual model will allow you to modify parameters such as thickness, color scheme, and resolution.
Want to focus on residues involved in binding? Highlight interactions on the solvent-excluded surface using the proper selection filter to limit your view to relevant atoms or residues.
Starting from Default and Going Beyond
SAMSON includes a curated set of default visual models that cover most common needs. But if those aren’t enough for your specific problem, it’s possible to go further. You can access additional ones through SAMSON Connect, and if you’re technically inclined, you can even develop your own visual model.
This modularity gives researchers a flexible way to adapt visualizations to their workflows. It also means that SAMSON isn’t just a platform for visualization—it’s a toolkit for building the visualization tools you need.
Why This Matters
For molecular modelers, manipulating structures visually is often the fastest route to insight. Whether you’re preparing slides for a talk or trying to validate the result of a docking simulation, having fast and powerful visual tools makes a difference.
Learn more from the official documentation here: https://documentation.samson-connect.net/users/latest/models/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here: https://www.samson-connect.net