Anyone working in molecular modeling or structural biology knows that dealing with complex systems often means juggling different layers of information: atomic coordinates, chemical bonds, visual styles, simulation data, annotations, and more. If this sounds familiar, you may be relieved to know there’s a well-organized system behind the scenes in SAMSON to make this all manageable: node types.
If you’ve heard the term “node” in SAMSON but wondered how it relates to your work, or how SAMSON even keeps track of a protein structure and its different representations, you’re not alone. Let’s dive into what node types are and how understanding them can make your molecular modeling workflow much more efficient and intuitive.
What Is a Node in SAMSON?
In SAMSON, everything you see or manipulate is a node: atoms, bonds, molecular models, measurement labels, cameras, visual representations, etc. Essentially, nodes are the basic building blocks of the SAMSON data graph. By combining different types of nodes, you can construct and analyze complex molecular systems.
OK, So What Are Node Types?
The Node Types reference page in the documentation provides a detailed listing of all node types used in SAMSON. These include (but are not limited to):
- Structural Nodes: atoms, residues, molecules, chains
- Visual Nodes: materials, representations (e.g., ball-and-stick models, surfaces)
- Document Nodes: annotations, selection groups, data containers
- Camera and rendering nodes
Knowing the type of a node helps SAMSON—and you—understand how to work with it, how it connects to other nodes, and what operations can be applied to it.
Why Does This Matter?
You might be asking: does this really impact how I build or analyze a molecular system? The answer is: yes, especially if you want to work efficiently.
Let’s say you want to programmatically select all atoms within 5 Å of a ligand. If you understand that atoms are a specific node type, you can use filters within SAMSON’s Node Specification Language (NSL) to target exactly what you want—without trial and error or selecting things one by one manually.
Understanding node types also becomes critical when you:
- Customize visual representations (apply a color to all residues, not just atoms)
- Script your analysis workflows (looping over node types programmatically)
- Debug complex systems (e.g., why is that surface not updating? Maybe it’s because you’re not targeting the right node type)
How Node Types Support Extensions
Another advantage is that when you’re using SAMSON Extensions, such as simulation or visualization tools, interactions depend heavily on node types. An Editor Extension may operate only on molecule-type nodes, for instance, and knowing this helps you apply tools efficiently and correctly.
Conclusion
If you’re trying to get the most out of SAMSON, especially when working with complex biomolecular systems, developing an awareness of node types can save you time, reduce errors, and make your analysis more precise. Node types are one of those behind-the-scenes concepts that quietly power everything you do in SAMSON.
For a full overview of the available node types and how they’re structured, check out the original documentation here: https://documentation.samson-connect.net/users/latest/node-types/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.