Whether you’re preparing molecules for docking, refining a visualization, or doing computational analysis, selecting specific subsets of atoms quickly — and accurately — can greatly improve your workflow. One group of atoms that’s both chemically significant and finicky to identify is aromatic atoms.
In the NSL of SAMSON, isolating aromatic atoms is simple and fast. This is particularly helpful when you’re working with large biomolecules or performing aromaticity-dependent tasks like stacking interaction analysis or calculating π-systems.
Why target aromatic atoms?
Aromatic atoms often play critical roles in molecular recognition and stability. You may want to:
- Highlight aromatic rings in a visualization for presentation or publication
- Identify atoms involved in π-stacking interactions
- Extract all aromatic carbons for quantum calculations or force field parameterization
Using NSL to Select Aromatic Atoms
In NSL, the attribute atom.aromatic (or its short form a.ar) matches atoms labeled as aromatic. To create refined selections, combine it with other attributes like atomic symbol.
Here are a few examples:
a.ar: selects all aromatic atomsa.s C and a.ar: selects only carbon atoms that are aromatica.s N, O and a.ar: selects aromatic nitrogen and oxygen atoms
Visual Spotlight: Highlight Aromatic Carbons
Let’s say you want to visually isolate aromatic carbon atoms in a protein ligand to focus your analysis. Here’s a simple NSL query:
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a.s C and a.ar |
This will match all carbon atoms that are defined as aromatic in your loaded structure. You can then apply a specific visualization style — like ball-and-stick or surface coloring — to this selection.
Scenarios Where This Selection Helps
- Pharmacophore mapping: Identify and extract aromatic groups to map potential ligand–receptor interactions.
- Aromaticity analysis: Select atoms for computational checks on aromaticity across chemical libraries.
- Ring-specific editing: Use selections to precisely modify or mutate aromatic rings in a molecular editor.
Combining with Other Filters
Need even more precision? Combine a.ar with spatial constraints or structural properties. For example:
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a.ar and a.x > 10A |
This matches aromatic atoms with x-coordinates beyond 10 angstroms — helpful when dealing with large, asymmetric systems.
Conclusion
The a.ar attribute in NSL simplifies the once tedious task of identifying aromatic atoms. With concise and flexible expressions, you can integrate aromatic selections directly into complex workflows, freeing up time for deeper analysis.
To learn more about all available atom attributes, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/nsl/atom/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.