A molecular scene can be confusing for a simple reason: the object you see may not be the object that defines the molecule. A ribbon, surface, or field visualization can change how a nanosystem appears without being the structural description itself. When you need to identify what a selected item does—or decide what to add next—it helps to distinguish the model categories in SAMSON.
Think of the categories as answering different questions. Structural models describe geometry and topology. Visual models provide graphical representations. Dynamical models describe degrees of freedom and store dynamical state. Interaction models provide energies and forces. Property models represent other properties. State updaters are related, but are not a sixth model category: they advance states during minimization or simulation.
Start with the problem you are trying to solve
- Need to describe what is physically organized? Look to structural nodes: atoms and bonds, with higher-level organization such as molecules, chains, and residues.
- Need to change how the structure is drawn? Look for a visual model. Examples include protein secondary-structure representations, Gaussian surfaces, isosurfaces, and volumetric field representations.
- Need to define motion? A dynamical model specifies where degrees of freedom are. For example, a particle-system dynamical model gives each atom three translational degrees of freedom.
- Need energies or forces? That is the role of an interaction model. Examples include Lennard-Jones, spring, elastic network, and universal force field models.
- Need to represent a quantity that does not fit the other categories? A property model can represent a number, scalar or vector field, or function.
This quick check helps avoid a common mix-up: a surface is usually a way to view or select a structure, not a substitute for the atoms and bonds that describe its topology. Similarly, an interaction model and a state updater play different roles: one provides energies and forces; the other advances the system’s state.
When the scene looks different, inspect the visual layer
SAMSON includes visual models that can be applied to selected nodes, or to the whole document when nothing is selected. You can add one through the selection’s context toolbar, through Visualization > Add > Visual model, or with Ctrl/Cmd + Shift + V. Some visual models also expose parameters in the Inspector. Select the visual model in the Document view and choose Inspect from its context menu to see whether those settings are available.
The examples below show why it is useful to treat visualization as its own layer: one structure can be represented in different ways, and a surface can also support highlighting and selection of underlying atoms, residues, or chains, depending on the selection filter.
A practical troubleshooting sequence
- Identify the selected node. Ask whether it represents structure, appearance, motion, interactions, or another property.
- Check the task. If you want a different appearance, try a visual model; if you need forces or a simulation setup, look at interaction and dynamical models instead.
- Inspect before changing. For visual models with adjustable parameters, use the Inspector to understand what can be modified.
- Keep simulation components distinct. Interaction models supply energies and forces, while state updaters advance states during minimization or simulations.
This mental map is useful when browsing a complex document because it separates what the system is, how it is shown, and how it can move or interact. For definitions and related workflows, see the SAMSON models reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.