Molecular modelers working on complex structures often face organizational challenges. How should different molecular elements be represented? How can they be grouped, manipulated, and visualized consistently? If you’ve ever felt lost trying to manage atoms, molecules, and annotations in your models, you’re not alone.
In SAMSON, this challenge is addressed elegantly through its underlying data model based on Node Types. Understanding this system can significantly enhance your modeling workflow, improve performance, and help you create clean, understandable project structures.
What are Node Types?
Everything you load or create in SAMSON is represented as a node in a hierarchical structure called the data graph. Each node in the graph has a type: for example, an atom, a bond, a molecule, an annotation, a camera, or even a simulation result output.
- Structural nodes: Atoms, bonds, molecules, residues, chains, etc. These represent the molecular structures you are working on.
- Visual nodes: These affect how structures are represented — for instance, visual models or visual presets that define colors and shapes.
- Functional nodes: Algorithms, simulations, or measurement tools.
- Meta nodes: Groups, folders, or annotations that help organize your data.
By combining nodes into hierarchies and substructures, SAMSON allows users to build highly structured, modular models. This is especially helpful when working with macromolecules, molecular assemblies, or large simulation results.
Why This Matters
Many modeling frustrations trace back to poorly organized project structures. For example:
- Running a simulation on the wrong subset of your model 💢
- Forgetting which parts were loaded, duplicated, or edited
- Mixing annotations or measurements with structural data
By knowing which node type you are working with, and how different node types interact, you can:
- Quickly select meaningful groups of atoms or residues
- Apply specific visual styles to specific parts of your model
- Run simulations only on intended subsets
- Document your design process with better structure
Helpful Tip: Use the Node Specification Language
Once you understand node types, you can make powerful use of SAMSON’s Node Specification Language (NSL). This lets you locate nodes based on their type and attributes. For example:
|
1 |
type = Atom and symbol = C |
This would select all carbon atoms in the system. Combine this with your node structure and you’ll be navigating large models with ease.
Conclusion
Mastering Node Types in SAMSON is a simple but powerful step toward better modeling. It improves clarity, reproducibility, and project manageability — things that every molecular modeler can benefit from.
Learn more about Node Types in the SAMSON documentation.
Want to try it out? SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.