Accurately visualizing molecular and nanoscale systems can be a challenge, especially when trying to distinguish between different chains, residues or fields in a dense model. This is a common pain point for molecular modelers who need to both inspect and present complex systems clearly.
SAMSON helps address this with an important feature: visual models. These models are not simply decorative—they actively support selection, presentation, and interpretation of nanoscale systems.
What Are Visual Models?
Visual models in SAMSON provide graphical representations of parts of your system. For example, they can display protein secondary structures, solvent-excluded surfaces, electron densities, and electrostatic fields using surfaces, volumes, and lines.
Key takeaway: Visual models are applied to structural nodes, like atoms or residues, to make features easier to see, interact with, and understand.
Common Uses of Visual Models
- Surface representations to identify boundaries and cavities
- Color mapping based on fields or atomic data
- Volumetric rendering for properties like electron density or electrostatic potential
- Highlighting selections for communicating structural or chemical features
By default, SAMSON comes with several predefined visual models such as ribbons for secondary structures, dot surfaces, and electrostatic field viewers. You can apply them selectively or globally, which is helpful for both exploration and visualization tasks.
Applying Visual Models in SAMSON
You can add a visual model in several ways:
- Using the context menu on a selected node
- Via the top menu: Visualization > Add > Visual model
- With a shortcut: Ctrl / Cmd + Shift + V
Once inserted, you can modify their parameters. Select the visual model in the Document view, right-click and choose Inspect. This opens the Inspector panel, where you can tweak settings like surface resolution, coloring schemes, and opacity.
Selecting Through Visual Models
Visual models in SAMSON aren’t just passively displaying information—they also allow for more intuitive selection. For instance, if you’re working with a solvent-excluded surface, you can directly click on regions of the surface to select underlying atoms or residues.
Make sure your selection filter is correctly configured to streamline that process.
Extending the Visual Model Library
You’re not limited to the default models. More visual models are available through SAMSON Connect, and you can even develop your own using SAMSON Extensions. This makes the system highly adaptable to specific modeling workflows.
Want to Dive Deeper?
For more detailed instructions and ideas on using visual models effectively, visit the official Visual Models documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.