Quickly Identify and Filter Side Chains by Atom Counts in SAMSON

When analyzing large biomolecular structures in SAMSON, one of the frequent challenges modelers face is how to effectively identify or isolate specific side chains based on their composition. Whether you’re interested in visualizing groups rich in nitrogen, filtering out hydrophobic side chains, or selecting charged moieties, doing this manually can be both time-consuming and error-prone 🧬.

The Node Specification Language (NSL) in SAMSON helps address this issue—in particular, through the use of the sideChain attribute space. This feature allows detailed selection and filtering of side chains based on their chemical and structural properties. In this post, we’ll focus on how to use the sideChain attributes to select side chains by atom counts and charges, easing your model exploration process.

Why this matters

Imagine you’re working on a protein-ligand interaction and would like to understand how the local environment varies in terms of charge or composition. Instead of scrolling through hundreds of residues, you can simply write a query like:

This will match all side chains with more than one nitrogen atom—a simple but powerful way to, for example, highlight polar or positively charged residues like arginine, lysine, or histidine.

Available Attributes for Side Chain Selection

The sideChain attribute space (sc) inherits properties from node and structuralGroup. Here are some of the most useful ones for atom-based filtering:

• sc.nC: Number of carbon atoms
• sc.nH: Number of hydrogen atoms
• sc.nN: Number of nitrogen atoms
• sc.nO: Number of oxygen atoms
• sc.nS: Number of sulfur atoms
• sc.fc: Formal charge
• sc.pc: Partial charge (float values)

These attributes make it easy to write powerful selection queries such as:

Use Cases

Let’s say you want to visualize side chains with negative formal charges, to examine acidic groups. Use:

Or, perhaps you’re interested in side chains rich in carbon (e.g., for mapping hydrophobic environments):

You can also combine attribute filters with visibility or selection flags, which are included in the sideChain attribute list. For instance:

This selects only the side chains currently visible in your model that contain more than one nitrogen atom.

A Void You Didn’t Know You Had

If you’ve been manually navigating complex molecular models or relying on visual guesswork, NSL brings much-needed precision to your process. It saves time, reduces mistakes, and helps you generate clearer insights from your simulations.

To explore more attribute options and their formats, refer to the official documentation.

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