Quickly Find Specific Chains Using NSL in SAMSON

If you’re working with large biomolecular systems in SAMSON, it can become overwhelming to manage and analyze specific chains. Whether you’re editing, visualizing, or preparing systems for simulations, refining your selection to just the relevant molecular chains can save significant time and reduce errors.

This post explains how to make your workflow more efficient by using the Node Specification Language (NSL) in SAMSON, focusing on attributes specific to molecular chains. In particular, we’ll explore how to filter chains based on chainID, numberOfResidues, numberOfSegments, and numberOfStructuralGroups.

Why Filter Chains?

Imagine you’re analyzing a multi-chain protein complex, or a protein-ligand-lipid system. You might need to hide, highlight, or isolate chains with specific structural properties. Instead of manually selecting chains (which becomes time-consuming as system size increases), NSL lets you select chains by logical conditions.

Let’s look into the attributes specific to chains and how you can use them efficiently in your queries:

🔹 chainID (c.id)

  • c.id 1 — selects chains with ID exactly 1
  • c.id 2:4,6 — selects chains with IDs 2, 3, 4, and 6

This is particularly handy when you’re interested in a known set of chain IDs after importing a structure from a PDB file.

🔹 numberOfResidues (c.nr)

  • c.nr > 130 — selects chains with more than 130 residues
  • c.nr 100:130 — selects chains with 100 to 130 residues

Use this when analyzing domain size or preparing systems only above or below certain thresholds in size.

🔹 numberOfSegments (c.ns)

  • c.ns <= 3 — selects simpler chains with low segmentation
  • c.ns 1:3 — good for filtering less fragmented models, such as single-segment proteins or peptides

This is particularly helpful when troubleshooting imported files with molecular discontinuities.

🔹 numberOfStructuralGroups (c.nsg)

  • c.nsg > 10 — selects chains rich in structural groups
  • c.nsg 10:13 — use it to narrow down chains based on internal complexity

Using this filter is useful when you’re performing structural analysis of specific chain topologies.

Combining Filters

Filters can be combined using Boolean operators in NSL to build more sophisticated queries like:

This selects chains that are longer (many residues) but less structurally diverse.

Practical Tip

Once a filter is applied, you can hide or show selected chains, assign materials, or analyze them independently. This streamlines workflows for tasks like binding pocket identification, structure simplification, coarse-graining, or molecular dynamics setup.

Explore more chain attributes and advanced queries in the full documentation:
https://documentation.samson-connect.net/users/latest/nsl/chain/

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

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