One of the challenges often faced by molecular modelers — whether they’re working in drug discovery, materials science, or structural biology — is managing the complexity of molecular data. In a large molecular system, how do you make sense of the hierarchy of atoms, residues, molecules, and their interactions? How can you perform targeted selections, apply transformations to specific parts, or organize your scene for clarity?
SAMSON‘s answer to this is pragmatic and elegant: everything is a node. In SAMSON’s design architecture, molecular structures, components, and even annotations are represented through a flexible and extensible node system.
So, what are nodes?
Nodes in SAMSON are the basic building blocks of any molecular design scene. There are different types of nodes for different entities, such as:
- Structural models: These represent entire molecular systems and their structure.
- Structural groups: Define subsets like protein chains or molecular fragments.
- Structural elements: Individual atoms, bonds, residues, etc.
- Visual models: Carry representation-specific information (e.g., Van der Waals surfaces, ribbons).
- Physical models: For simulating behaviors such as force fields or dynamics.
- Paths, shapes, graphs: Useful for interaction analysis and quantitative modeling.
Because all of these are nodes, they can be connected in a hierarchy — meaning you can navigate from a molecule down to each of its atoms, or select a group of residues and apply a transformation or color change.
Why does this matter?
The node types system helps manage complexity in several key ways:
- Selection logic: Need to select all water molecules, side chains in a specific domain, or atoms within a binding site? The node system helps structure those queries using advanced tools like the Node Specification Language (
NSL), which can access and filter specific node types based on properties. - Modularity: Since everything is a node, you can apply transformations, hide/show options, colors, and other operations to custom hierarchy levels — all without hardcoding behavior.
- Extension-friendly: When creating your own SAMSON Extensions, knowing how nodes are organized is the basis for writing efficient, performant apps or editors that work across structural models and simulations.
Example
Imagine importing a protein-ligand complex. The protein backbone is organized as structural groups and residues, the ligand as another molecule node, and interactions (e.g., hydrogen bonds) as edge nodes in an interaction graph. You wish to color the ligand atoms by atom type, and apply a ribbon representation to the protein backbone. Thanks to SAMSON’s node system, this task is straightforward and reproducible across different systems.
Where to go from here?
A full list and detailed description of SAMSON node types is available in the reference documentation. If you’re starting to script in NSL, build an extension, or simply want more control over complex molecular systems, this is one of the most valuable pages to know about.
Explore the list of node types in the SAMSON Docs
To learn more about the structure of the SAMSON documentation, see the full references index:
https://documentation.samson-connect.net/users/latest/references/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.