Quickly Find Molecules by Chain, Residue, or Structural Complexity

As molecular models grow in complexity, browsing and filtering them becomes a significant challenge. Whether you’re navigating large biomolecular systems or working with coarse-grained representations, it’s often difficult to isolate exactly what you need: a protein with three chains, a small molecule with fewer than 200 atoms, or a compound composed of a specific number of structural groups.

This is where the Node Specification Language (NSL) in SAMSON becomes extremely handy. Specifically, the molecule attribute space offers powerful tools for molecular modelers to filter and select molecules using straightforward expressions tied to meaningful molecular properties. Here’s how you can use it to streamline your workflow 🔍

What the molecule attribute space offers

The molecule attribute space (short name: mol) includes attributes specific to molecules, enabling you to query nodes based on core molecular characteristics. It allows you to compose queries like:

• mol.nr > 130 — number of residues greater than 130
• mol.nsg 10:13 — number of structural groups between 10 and 13
• mol.nc < 3 — fewer than 3 chains

Let’s explore some of the most useful attributes:

📌 Number of Chains (mol.nc)

This attribute matches molecules with a specific number of chains. This is useful for distinguishing between monomeric, dimeric, or multimeric proteins.

Selects molecules with fewer than three chains — for example, monomeric or homodimeric structures.

📌 Number of Residues (mol.nr)

You can filter out small ligands or large proteins by setting boundaries on the number of residues. For instance:

This matches molecules with residue count between 100 and 130 — useful for medium-sized domain identification or rational selection during modeling.

📌 Number of Structural Groups (mol.nsg)

Filters based on the level of subdivision within molecules. Structural groups may represent functional domains or specific regions depending on the model.

This helps identify complex molecules with multiple functional compartments.

Other filters include:

• Segments: mol.ns — isolates segmented domains in a molecule.
• Coarse-grained atoms: mol.ncga — targets models with reduced detail for faster simulation.

Combining Filters

These filters become more powerful when combined with logical operators. For example:

This matches large proteins with fewer chains — potentially good candidates for structural simplification or chain comparison.

Why this matters

Molecular complexity has its merits, but so does finding exactly what you need without navigating clutter. The molecule attribute space gives you the ability to be precise in your queries, save time, and keep your focus on research rather than repetitive selection clicks.

To learn more and explore the complete list of molecule attributes, visit the full SAMSON documentation page: https://documentation.samson-connect.net/users/latest/nsl/molecule/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.