Quickly Select Chains by Properties in SAMSON Using the NSL

Working with molecular models that include multiple chains can often feel overwhelming—especially if you’re trying to select or isolate specific chains based on unique criteria. Whether you’re preparing a simulation, analyzing a structure, or simply cleaning up a model, being able to select chains based on their properties can save you hours of manual clicking and filtering.

The Node Specification Language (NSL) in SAMSON offers a powerful way to automate this process. In this post, we’ll explore how you can use chain attributes to precisely target chains of interest in your molecules using NSL queries.

Why This Matters

Imagine a protein complex with multiple chains, but you only want to:

• Select chains visible in the viewport
• Work on chains with more than 100 residues
• Analyze chains rich in certain atom types

Doing this manually is tedious and prone to error. With the chain attribute space in NSL, it’s just a line of text away.

Example: Selecting Chains by Number of Residues

Suppose you want to select chains that contain more than 130 residues. You can use the following expression:

Need to specify a range? Use:

This instantly highlights chains in that range. It’s accurate and incredibly fast.

Combine Attributes for More Complex Filtering

Let’s say you’re looking for chains that:

• Are visible
• Have fewer than 3 segments

Try this:

Identify Chains by Specific ID

Perhaps you’re comparing specific chains across multiple models. Use the chainID:

This matches the exact chain. To select chains 2 through 4 and another at ID 6, you can write:

Other Useful Properties

• c.fc: Formal charge
• c.nC, c.nO, c.nS: Number of Carbon, Oxygen, Sulfur atoms
• c.ncga: Coarse-grained atom count

Want to quickly find chemically unique chains in a model? Just filter by atom type counts or formal/partial charge ranges.

Putting It All Together

Let’s consider a more advanced use case: You want chains that are hidden, contain 10–20 Oxygen atoms, and have more than 10 structural groups:

This is the power of NSL in action—precise targeting without clicking through menus.

To view the full list of attributes and learn more about how to use them, visit the documentation page here.

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