When you’re modeling large biomolecules, it’s not uncommon to find yourself overwhelmed by the number of elements in your scene—atoms, residues, chains, backbones, materials, and more. Sometimes all you want is to quickly isolate certain backbone fragments, say, those with a specific charge or number of atoms, and manipulate or analyze them.
The Node Specification Language (NSL) in SAMSON gives you this power—and if you work with molecular backbones, the backbone attribute space might be exactly what you didn’t know you needed.
Why this matters
Molecular modelers often work with complex systems. Whether you’re preparing a system for simulation or visualizing substructures, you need fast ways to filter and select only what matters. Instead of clicking your way through hundreds of nodes, being able to query with something like bb.nH < 10 can save time and reduce manual errors.
What is the backbone attribute space?
The backbone attribute space (short name: s) in SAMSON’s NSL matches backbone nodes and exposes a set of attributes that you can use for querying. These attributes include visibility, material presence, name patterns, selection state, and several chemical descriptors such as the number of atoms, partial charges, or formal charge.
Examples that simplify life
Here are some practical examples of NSL expressions you can try to filter backbones:
bb.nC 10:20– Select backbones with 10 to 20 carbon atoms.bb.fc > 0– Highlight positively charged backbone groups.bb.v– Returns all visible backbones.not bb.v– Quickly find hidden backbones in your scene.bb.n "A*"– Match all backbone nodes whose name begins with “A”.bb.pc 1.5:2.0– Filter nodes with partial charges in a specific range.
These expressions can dramatically simplify your workflows, especially during structure preparation, cleanup, or when focusing on specific substructures during analysis.
How this connects to other attribute spaces
Many of these attributes are inherited from node or structuralGroup attribute spaces. This means attributes like hasMaterial, visible, or numberOfAtoms don’t need to be defined again for backbone elements—they’re already available as part of their node hierarchy.
Beyond selection
Attribute filtering isn’t just for selection. Once you’ve refined your scene down to exactly what you’re interested in, you can feed these query results into other SAMSON Extensions—for rendering, exporting, scripting, or analysis workflows.
It’s a lightweight but powerful way to manage complexity without cluttering your user interface or pipeline.
To learn more about the full set of backbone attributes and filter options, head over to the official documentation: https://documentation.samson-connect.net/users/latest/nsl/backbone/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.