A molecular structure can be correct while its on-screen appearance is confusing—or look polished while lacking what a simulation needs. That mismatch is a common source of wasted effort: changing the display when the underlying structure is the issue, or looking for simulation behavior in a visual representation.
A useful first step is to ask what you are trying to change. In SAMSON, nanosystems are described using five model categories. Each answers a different question, so identifying the question helps narrow down the right kind of model.
Start with the object you want to change
- Structural models: What is the system made of, and how is it connected? These describe geometry and topology, typically using atoms and bonds, with higher-level organization such as molecules, chains, and residues.
- Visual models: How should the system be drawn? These provide graphical representations, such as a protein’s secondary structure, a Gaussian surface, an electron-density isosurface, or a volumetric electrostatic field.
- Dynamical models: Which parts can move, and what is their dynamical state? For example, a particle-system dynamical model assigns three translational degrees of freedom to each atom and stores positions, momenta, and masses.
- Interaction models: What energies and forces act on the degrees of freedom? Examples include Lennard-Jones, spring, elastic-network, and universal force-field models.
- Property models: What other information should be represented? Examples include a protein’s gyration radius, a scalar field, a vector field, or a function.
This distinction is especially useful when something seems “wrong” in the Document view. If the bonds or organization are wrong, inspect the structural representation. If the structure is there but the picture is not communicating what you need, consider a visual model instead. A visual model changes the graphical representation; it is not, by itself, a replacement for the structural description.
Make a display change without confusing it with a structure change
SAMSON includes visual models by default, and more can be added through SAMSON Connect. 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.
Some visual models expose parameters in the Inspector. To check whether that applies, select the visual model in the Document view and choose Inspect from its context menu. This is a useful route when the representation is the thing you want to adjust, rather than the molecular structure itself.
Visual models can also support selection: SAMSON’s default visual models make it possible to highlight and select atoms, residues, chains, and other elements directly on surfaces, depending on the active selection filter. If clicking the visible surface selects an unexpected kind of object, check the selection filter before assuming that the structure or surface is incorrect.
Keep simulation components distinct
For simulation, the key distinction is between describing motion and describing its causes. A dynamical model describes degrees of freedom and stores dynamical state; an interaction model supplies energies and forces corresponding to those degrees of freedom. A state updater is a separate component: it advances the state during a simulation or minimization, using methods such as molecular dynamics, Monte Carlo, or minimization algorithms.
In practice, this gives you a simple diagnostic: ask whether your task concerns the system’s composition, its appearance, its possible motion, the forces on that motion, or some other property. Those are different jobs, and SAMSON represents them with different node types. Matching the job to the model category makes it easier to find the right tool—and to avoid changing a display when you meant to change the science, or vice versa.
For details on the model categories and related workflows, see the SAMSON models reference.
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