A molecule is visible in the Document view, but something still seems off: the representation is missing, the system does not respond as expected, or it is unclear which item to select. These problems can be difficult to diagnose when every component is simply called a “model.” In SAMSON, the useful first question is more specific: what job should this model be doing?
SAMSON separates nanosystem information into five model categories. They are not five ways of drawing the same thing: each describes a different aspect of the system. Keeping those responsibilities distinct can help you identify what to inspect or add next.
A quick map of the five categories
- Structural models describe geometry and topology: typically atoms and bonds, with higher-level organization such as molecules, chains, and residues.
- Visual models provide a graphical representation, such as a protein secondary-structure view, a surface, or a field visualization.
- Dynamical models indicate where the degrees of freedom are and describe the dynamical state. For a particle system, for example, each atom can have three translational degrees of freedom. Dynamical models store positions, momenta, and masses.
- Interaction models represent energies and forces associated with a dynamical model. Examples include Lennard-Jones, spring, elastic network, and universal force field models.
- Property models represent other properties that do not belong to the first four categories, such as a gyration-radius value or a scalar or vector field.
A related component is the state updater. It is not a sixth model category: it implements methods for advancing states during simulations, including minimization, Monte Carlo, and molecular dynamics algorithms.
Diagnose the task, not the label
If you are trying to understand why something is not displayed as you expect, start with the visual layer. A structural model describes the molecular geometry and topology; a visual model supplies a graphical representation of it. In other words, seeing the structure and choosing how it is drawn are separate concerns.
SAMSON provides default visual models, and additional ones can be added from SAMSON Connect. Visual models are usually applied to selected nodes, or to the whole document when nothing is selected. You can access them through the selection’s context toolbar or via Visualization > Add > Visual model. The shortcut is Ctrl/Cmd + Shift + V.
If the representation is present but its appearance needs adjustment, some visual models expose parameters in the Inspector. Select the visual model in the Document view, then choose Inspect from its context menu. This is a useful distinction: you may need to inspect the visual model rather than the structural nodes it represents.
If your goal is to simulate or minimize a system, think in terms of a different chain of responsibilities. The dynamical model describes the degrees of freedom and state; the interaction model provides the associated energies and forces; and the state updater advances the state using a method such as molecular dynamics or minimization. These components answer different questions, so changing a visual representation is not the same as changing the forces or the way a simulation advances.
A practical check before changing anything
- What are you looking at? Atoms, bonds, molecules, chains, and residues belong to the structural description.
- What should be visible? Look for a visual model that provides the representation you want.
- What should be able to move or change? Consider the dynamical model and its degrees of freedom.
- What should drive that change? Check the interaction model’s role in providing energy and forces.
- How should the state advance? Identify the state updater used for the minimization or simulation workflow.
This simple checklist helps avoid troubleshooting the wrong layer—for example, adjusting a drawing when the question is about dynamics, or expecting an interaction model to act as the simulation algorithm.
For the complete reference, see Models in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.