A molecular scene can show atoms, surfaces, fields, forces, and motion-related information side by side. When you select an item in the Document view, it is not always obvious what role it plays: does it describe the molecule’s structure, change how that structure is drawn, or contribute to a simulation? Mixing these roles up can make it harder to understand or edit a document.
A useful first step is to ask what the selected item represents. In SAMSON, models fall into five categories. Each answers a different question about the nanosystem.
Start with the five questions
- Structural model: What is there, and how is it connected? Structural models describe geometry and topology. They typically contain atoms and bonds, and may include higher-level nodes such as molecules, chains, and residues.
- Visual model: How should it be shown? Visual models provide graphical representations, such as a protein’s secondary structure, a Gaussian surface, an electron-density isosurface, or a volumetric electrostatic field.
- Dynamical model: What can move, and what state does it have? Dynamical models indicate degrees of freedom in structural nodes and store positions, momenta, and masses. For example, a particle-system dynamical model assigns three translational degrees of freedom to each atom in the particle group.
- Interaction model: What energies and forces act? Interaction models provide energies and forces associated with a dynamical model. Examples include Lennard-Jones, spring, elastic-network, and universal force-field models.
- Property model: What other information is attached? Property models represent properties outside the first four categories, such as a gyration-radius value, a scalar or vector field, or a function.
Why appearance can be misleading
A surface or ribbon-like representation may look like the molecule itself, but it is a visual model: it provides a way to see structural information. The structural model describes the geometry and topology. Keeping those roles separate helps when you want to change how a scene looks without confusing that action with changing what the molecular structure contains.
SAMSON’s default visual models can represent structures in different ways. The examples below show some available representations:
Visual models are usually applied to selected nodes, or to the whole document when nothing is selected. You can add one from the selection’s context toolbar, through Visualization > Add > Visual model, or with Ctrl/Cmd + Shift + V. For some visual models, selecting the model in the Document view and choosing Inspect opens visualization parameters in the Inspector.
For example, a surface can also support selecting or highlighting atoms, residues, or chains, depending on the active selection filter. That interaction with a surface does not make the surface the structural model; it remains a visual representation used to view the structure.
Keep simulation components distinct
Three categories often appear together in modeling and simulation workflows, but they do different jobs. The dynamical model describes degrees of freedom and state; the interaction model supplies the corresponding energies and forces; and a state updater advances the state during a simulation. State updaters are not one of the five model categories. They implement methods such as minimization, Monte Carlo, or molecular dynamics algorithms.
When a document feels confusing, try classifying each selected node by its job rather than by its name or appearance: structure, display, dynamical state, energy and force, or another property. That small check can clarify what you are inspecting and which part of a workflow you need to adjust.
For the full reference, see Models in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.