Finding Aromatic Atoms Quickly in Molecular Models with NSL

Molecular modelers often need to identify specific atomic features in complex structures, such as aromatic rings, metal atoms, or nucleic acid backbones. A common challenge is selecting atoms with shared chemical characteristics without manually inspecting or guessing their positions. This is especially tedious when analyzing large biomolecular systems or preparing models for simulations.

The Node Specification Language (NSL) in SAMSON addresses this pain by providing an efficient, readable syntax to express atom-level queries. One especially useful capability is selecting aromatic atoms.

Why would you want to select aromatic atoms?

Aromatic atoms are involved in π-systems that are essential to biological function, drug interactions, and molecular recognition. For example:

• Identifying hydrogen-bonding or stacking partners in a protein-ligand complex
• Applying specific parameters to pi-systems in quantum calculations
• Filtering atoms that belong to aromatic rings for visualization or analysis

Using NSL to select aromatic atoms

NSL provides a simple, expressive way to query for atom properties. To select aromatic atoms, use the aromatic attribute (a.ar):

This matches any atom that is marked as aromatic.

To further refine your selection, for instance if you only want aromatic carbons, combine conditions:

The short name for atom.symbol is a.s, and for aromatic, it’s a.ar. This query matches all carbon atoms that are aromatic.

Visual example: NSL table entry

Here’s the relevant portion from the documentation, with examples provided:

Examples:

• a.ar – matches all aromatic atoms
• a.s C and a.ar – matches aromatic carbon atoms

Combining with other filters

You can combine the aromatic attribute with other filters. For example, to find aromatic atoms that are not in metal subgroups:

Or, to find aromatic atoms within a particular chain:

These combinations are very handy when navigating complex biomolecules or visualizing pharmacophores.

Learn more

NSL helps you move away from manual filtering and empowers you with precise and reusable atom selection logic. Learn more on the full atom attributes documentation page: NSL Atom Attributes Documentation.

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