If you’ve ever found yourself buried under a complex molecular system and unsure how to efficiently interact with its components in SAMSON, the answer might lie in understanding Node Types. Mastering node types is key to organizing, manipulating, and visualizing molecular data in a meaningful and efficient way—and it can dramatically improve your workflow when designing or simulating molecular systems.
What are Node Types?
In SAMSON, everything you see in your workspace—atoms, molecules, visual models, simulation outputs, annotations—is represented as a node. The Node Types documentation categorizes the different kinds of nodes, helping users better understand what they can do and how each node behaves.
Nodes are the fundamental building blocks of the SAMSON document structure. They contain data and define how objects relate to each other. For example:
- Structural Model Nodes: Represent the hierarchy of atoms, bonds, molecules, and larger assemblies.
- Visual Model Nodes: Responsible for the graphical representation of other nodes (e.g., rendering atoms as spheres or ribbons).
- Simulation Model Nodes: Define the behavior and rules, such as force field parameters or custom dynamics.
- Group Nodes: Useful for organizing multiple nodes under a common parent node for easier manipulation.
This modular structure allows for a clean separation of semantics (what something is) from appearance (how it’s displayed) and behavior (how it moves or interacts). Whether you’re developing a new molecular model, scripting simulations, or building complex scenes, understanding which node type you’re working with helps you avoid unnecessary complications.
Why It Matters
Users often face confusion when their selections target the wrong nodes, or when visualization appears disconnected from the data. By learning which node is responsible for what, you can resolve these issues quickly:
- Struggling to change how your model looks? Maybe you’re editing the structural node instead of the visual model node.
- Can’t apply physics to a structure? You might be missing the correct simulation model node for your object.
- Want to export only a subset of a model? Use group nodes to isolate parts of the hierarchy.
Hidden Gems: Specialized Node Types
SAMSON also supports specialized nodes such as interaction models or manipulators. For example, the Interaction Designer allows you to create interactive molecular simulations by combining different node types.
Another advanced feature is the Node Specification Language (NSL), which lets you perform complex queries on node types. For example, you could select all atoms within a certain distance of a certain residue, based purely on node characteristics.
A Quick Tip
Try exploring your current SAMSON document with the “Document View” to see the node hierarchy. Right-clicking on nodes allows context-specific actions like creating new subnodes, changing visual presets, or attaching simulation models. The more familiar you are with what types of nodes you’re using, the more powerful your modeling becomes.
If you’d like to learn more about the different types of nodes and how to use them, refer to the original documentation here: https://documentation.samson-connect.net/users/latest/references/.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.