Whether you’re building biomolecular structures, simulating protein-ligand interactions, or designing nanomaterials, understanding how your data is structured can save you time and reduce errors in your workflow. In SAMSON, one of the key organizational concepts is the Node.
Nodes are the basic building blocks of molecular models in SAMSON, and the platform relies on a flexible node-based architecture to represent everything from individual atoms to entire simulation trajectories. At a glance, this might seem like a technical detail—but for molecular modelers, it can be the difference between a smooth modeling experience and a frustrating one.
What Are Node Types?
SAMSON represents molecular systems as hierarchical structures of nodes. Each node type corresponds to an element of your model—like atoms, bonds, groups, molecules, or even visual elements and simulation results. Understanding node types lets you:
- Quickly navigate large molecular systems
- Apply selections based on node characteristics
- Use the SAMSON Interaction Model more effectively
- Filter and group different parts of your system for advanced operations
For example, you might want to select all molecules in a certain chain, or all atoms belonging to a particular residue type. This becomes easier when you’re familiar with the node hierarchy and the roles of different node types.
Common Node Types You Should Know
- Structural nodes: These include atoms, groups, residues, chains, molecules, etc. When building or editing structures, these are your main components.
- Visual models: Control how structures appear—e.g., ball-and-stick or surface representations. Not modifying the model, but crucial for analysis and communication.
- Simulators and results: Nodes can also encapsulate simulation results, force fields, animations, and more, enriching your model with interactive data.
When the Structure Matters Most
Imagine trying to run an energy minimization on only a subset of a molecule or rendering a surface for a specific protein domain. Without understanding how nodes are organized, selecting exactly what you need becomes tedious. But if you know how node types are arranged, these actions become a matter of a few clicks or a single selection command.
Bonus: Node Types + NSL = Powerful Selections
Once you’re comfortable with node types, you’ll get much more out of the Node Specification Language (NSL), which lets you write expressive queries like:
|
1 |
> atom.element C and residue.name ALA |
This selects all carbon atoms belonging to alanine residues, for example. You can mix and match property selectors with logical operators to interrogate even big biomolecular systems effectively.
Useful Tip
Need to inspect the hierarchy of your system? Use the Document View in SAMSON’s interface to explore all nodes in your current document. Right-clicking on nodes reveals context-sensitive actions like renaming, grouping, or changing visual styles.
To explore all the available node types and how they interact in SAMSON, check the full reference at the link below.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.