When working with complex molecular systems in SAMSON, one of the most common frustrations is navigating your model efficiently. For newcomers and experienced users alike, it’s easy to get overwhelmed by the variety of molecular elements, annotations, and visual representations—and even easier to lose track of how they’re structured. That’s where node types come in.
Understanding node types can significantly reduce time spent searching through your document hierarchy, selecting the right elements, or figuring out why certain objects don’t behave as expected. This blog post will break down what node types are, why they matter, and how using them correctly can make your life easier.
What Are Node Types in SAMSON?
Everything in a SAMSON document is a node. At a high level, nodes organize the molecular system you’re working on. Node types refer to the specific roles that these nodes play—ranging from atoms and bonds to models, labels, groups, and even selections.
Here are a few major categories of node types you’ll encounter:
- Structural node types: atoms, residues, molecules, and structures.
- Model node types: used to represent calculated or predicted data (like an electrostatic potential map).
- Group node types: allow logical organization of various nodes, useful for structuring large assemblies.
- Label node types: visual annotations that help in understanding molecular layout.
- Selection node types: predefined or dynamic selections that can accelerate repeat tasks.
Why It Matters
Let’s say you’re modeling a protein-ligand complex and want to run an analysis only on the protein atoms. If you understand how node types are structured, you can directly filter or operate on nodes of type ‘Atom’ within your protein group using powerful tools like the Node Specification Language (NSL). If not, you might find yourself pointing and clicking through a sea of atoms manually—and making mistakes along the way.
Beyond that, using node types effectively allows you to:
- Quickly apply styles or visual presets to only certain parts of your model
- Write reusable scripts or selection queries
- Import/export relevant subsets of your model
- Debug unexpected behaviors (e.g., why a simulation fails due to an unrecognized node type)
Tips for Using Node Types Efficiently
- Use grouping: Organize sets of related nodes (e.g., all ligands, water molecules) into named groups using group nodes.
- Leverage the NSL: The Node Specification Language allows advanced selection based on node type, label, or hierarchy.
- Inspect types: Right-click on any item in the Document view and use Inspect node to see its type and properties.
- Filter selections: Always double-check what node type your selection tools are targeting, especially when applying transformations or visual effects.
Conclusion
Node types are not just technical details—they’re essential for efficient modeling, accurate analyses, and effective communication. Investing a bit of time to understand them will dramatically improve your workflow in SAMSON.
You can explore the full documentation on node types here, or browse other helpful topics in the SAMSON Reference documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.