Easily Select Chains by Residue Count in Your Molecular Models

A common challenge when working with complex biomolecular systems is efficiently identifying and selecting chains based on their characteristics. Suppose you’re analyzing a protein–protein interaction, or refining a molecular assembly, and want to focus only on chains that are sufficiently long (or short). Manually examining dozens or even hundreds of chains becomes unmanageable very quickly.

If you’re using SAMSON, its Node Specification Language (NSL) provides a concise solution to this issue. Specifically, the numberOfResidues attribute in the chain attribute space makes this task both quick and precise.

Why filter by number of residues?

Residue count is a practical proxy for chain length. Whether you’re scanning for small peptides, ignoring scaffolding sequences, or trying to isolate large chains for further structural analysis, filtering by residue count saves time and reduces clutter.

The syntax is straightforward using NSL. Let’s walk through the key components and examples.

Using c.nr to filter chains

In NSL, the chain attribute for number of residues is accessible with the short name c.nr. This attribute accepts integers, and several operators and range patterns are permitted:

  • c.nr > 100 — matches chains with more than 100 residues
  • c.nr 100:120 — matches chains with between 100 and 120 residues, inclusive

This enables you to ignore short peptide fragments or, alternatively, select only small chains if that’s your focus.

Example use cases

  • Identify large domains: c.nr > 250 filters for domain-sized chains and larger.
  • Detect small interface chains: c.nr <= 50 targets small peptides, often domains of interaction.
  • Screen chains of specific size: c.nr 75:90 is useful when evaluating designed sequences within a narrow window.

For more nuanced selections, you can combine this attribute with others, such as c.h (hidden), c.vf (visibility flag), or c.n (name).

Where to find this in the documentation

The numberOfResidues attribute is a chain-specific property explained in the chain attributes section of the Node Specification Language guide. This tool is a valuable resource not only for selection, but also for automating workflows and scripting structural queries in SAMSON.

To learn more, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/chain/

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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