When a molecular scene looks wrong—or simply behaves differently than expected—it is tempting to assume the molecule itself is the problem. But a SAMSON document can contain several kinds of models, each with a different job. A surface, a set of atoms, and the forces used in a simulation are not interchangeable representations of the same thing. Knowing which category you are looking at can help you find the right place to inspect or make a change.
A useful first question is: is this about structure, appearance, motion, forces, or another property? Those questions map to SAMSON’s five model categories.
Start with the structure
Structural models describe geometry and topology: the components of a nanosystem and how they are organized. They typically contain atoms and bonds, and may include higher-level nodes such as molecules, chains, and residues. If your question is “Which atoms are connected?” or “What residues make up this chain?”, you are thinking about the structural model.
This distinction is useful when a visual change seems to affect the science. A different drawing of a molecule is not, by itself, a change to its atoms or bonds. First identify whether the object you selected represents the structure or how the structure is drawn.
Separate what you see from what is modeled
Visual models provide graphical representations. Examples include secondary-structure representations, Gaussian surfaces, electron-density isosurfaces, and volumetric views of fields. They answer “How is this being displayed?” rather than “What is the underlying connectivity?”
SAMSON’s default visual models 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 have parameters available in the Inspector: select the visual model in the Document view and choose Inspect from its context menu.
Visual models can also support selection. The default models make it possible to highlight and select atoms, residues, or chains directly on surfaces, depending on the active selection filter. If clicking a surface selects an unexpected kind of object, check the selection filter as well as the visual model.
When the question is about motion or energy
Dynamical models indicate where degrees of freedom are in structural nodes and describe the dynamical state. For a particle system, for example, a dynamical model can assign three translational degrees of freedom to each atom. Dynamical models store quantities such as positions, momenta, and masses. If your issue concerns what can move, or the state being used during a simulation, this is the category to consider.
Interaction models represent energies and forces associated with a dynamical model. Examples include Lennard-Jones, spring, elastic network, and universal force-field models. An interaction model provides forces corresponding to the degrees of freedom; for a particle system, it can provide the total energy and the force on each particle. So, when you are asking “What is pushing or pulling these atoms?” look to the interaction model rather than the visual representation.
Where do other values belong?
Property models represent properties not covered by the first four categories. Examples include a gyration-radius value, a scalar field such as electron density, a vector field such as an electrostatic field, or a function. This category is a reminder that useful molecular information is not always a structure, display, motion definition, or force calculation.
A quick way to narrow it down
- Atoms, bonds, organization? Structural model.
- Rendering, surface, or representation? Visual model.
- Degrees of freedom or stored dynamical state? Dynamical model.
- Energy or forces? Interaction model.
- Another value or field? Property model.
Finally, keep state updaters distinct from these five categories. They implement methods for advancing states during simulations, including minimization algorithms, Monte Carlo methods, and molecular dynamics algorithms. A helpful mental sequence is: structure defines what is there; dynamical models describe what can move; interaction models calculate energies and forces; state updaters advance the state; visual models determine how the result is shown.
For definitions and related workflows, see the SAMSON model reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.