Quickly Select Specific Elements in SAMSON Using Atom Attributes

When modeling large biomolecular systems, selecting specific atoms by element is something molecular modelers often need to do. Whether you’re isolating carbon atoms for visualization, analyzing metal ions in a binding pocket 🧲, or simulating solvent interactions with polar oxygens, being able to filter atoms based on their chemical nature saves time and reduces errors.

If you use SAMSON for molecular design, the Node Specification Language (NSL) makes this task straightforward. In this blog post, we’ll walk through how you can use the element and symbol attributes to select atoms efficiently and unambiguously.

What’s the difference between element and symbol?

Both attributes relate to the identity of atoms, but they operate on slightly different naming conventions:

• element uses the full name of the chemical element (e.g., Carbon, Nitrogen)
• symbol uses the standard chemical symbol (e.g., C, N)

So, for example:

• a.e Carbon selects carbon atoms using their name.
• a.s C selects carbon atoms using their symbol.

These attributes can be very helpful when you only want to work with specific atoms—even in highly complex molecular assemblies.

Examples That Save Time

Let’s dive into some practical queries using the NSL syntax for various use cases:

1. Select all oxygen atoms

Alternatively, using symbol:

2. Select all carbon and nitrogen atoms

Or using symbols:

3. Focus on halogens only (e.g., Fluorine, Chlorine, Bromine)

4. Select rare metals, such as Zinc or Iron

5. Combine with other attributes: Aromatic Carbons

This last example shows how powerful combinations can be. You’re not just selecting carbon atoms—but only those involved in aromatic systems, possibly part of an active site.

Why This Matters

When dealing with complex structures, having to visually inspect and manually select atoms introduces bottlenecks and often errors. With NSL expressions like a.e and a.s, selections become scriptable, error-proof, and repeatable. You can also incorporate them into automation workflows for analysis, simulations, and visualizations.

Whether you’re filtering atoms to calculate partial charges, visualize specific functional groups, or prepare input for quantum calculations, knowing how to use these base-level selectors is a foundational step.

Learn More

Check out the full SAMSON documentation for atom attributes and examples at 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.