Quickly Find the Chains You’re Looking For with NSL

Anyone working with complex molecular models knows how quickly a project can become overwhelming. Once you have large protein structures, assemblies, or entire molecular systems with multiple chains, managing and navigating them effectively becomes a challenge. What if you’re only interested in chains that are visible, contain more than 100 residues, and are tagged with specific IDs? Scrolling through the structure manually isn’t scalable.

This is where the Node Specification Language (NSL) in SAMSON shines. In this post, we’ll look at how chain attributes in NSL can help you filter and query chains based on insightful criteria, saving you time and reducing the noise in your molecular modeling workflow.

Why filtering chains matters

In projects involving large biomolecules or simulations, you may want to:

  • Focus on biologically relevant chains (e.g., main protein chains, excluding glycosylation tails)
  • Select only visible chains to create publication-ready visualizations
  • Analyze only those chains that contain above a certain number of residues

Rather than hunting for these manually, NSL lets you make expressive queries very quickly.

Key NSL attributes for chains

The chain-related attribute space in NSL is referred to with short prefix c. Here’s a practical breakdown of commonly used attributes for filtering chains:

  • Visibility: c.v — matches visible chains
    c.v (visible), not c.v (not visible)
  • Chain ID: c.id — useful if you want specific identifiers
    c.id 1 or c.id 2:4,6
  • Number of residues: c.nr — helps filter chains by size
    c.nr > 100 (chains with more than 100 residues)
  • Number of segments: c.ns — chain complexity metric
    c.ns 1:3
  • Name: c.n — match chain names
    c.n "A" or patterns like c.n "L*"

Combined together, these filters can give precise control. For example:

This expression matches visible chains that contain more than 120 residues and have chain IDs from 1 to 5.

Filtering by composition

If you’re interested in chemical composition, you can also use attributes like:

  • c.nC: number of carbon atoms
  • c.nH: hydrogen count
  • c.partialCharge (c.pc): partial charge values

This allows you to filter chains with high negative or positive charge, or a larger hydrocarbon presence.

Try it on your own structures

Whether you’re preparing systems for simulations or cleaning up views for presentations, using NSL with chain attributes improves clarity and boosts efficiency. Instead of manual selections and trial-and-error, you gain precision with a single line. Take some of your current projects and try filtering out chains using these attributes—you might be surprised how much clutter you can eliminate.

To learn more and view the full list of chain attributes, refer to the official SAMSON documentation on chain attributes in NSL.

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

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