How to Select Chains by Atom, Residue, or Segment Counts in SAMSON

When exploring complex biomolecular systems, being able to efficiently select and manipulate specific chain structures is essential for insightful analysis. Whether you’re visualizing protein assemblies, preparing systems for simulation, or filtering out unwanted models, having control over chain-level attributes can save hours of repetitive work.

In SAMSON, the integrative molecular design platform, chain nodes come with a rich set of attributes you can directly query using the Node Specification Language (NSL). A common user frustration is trying to isolate chains that meet structural criteria, like containing a certain number of residues or having too many atoms.

In this post, we highlight a fast and precise way to select chains based on attributes such as:

• Number of residues (c.nr)
• Number of segments (c.ns)
• Number of structural groups (c.nsg)
• Number of atoms (c.nat)

Let’s take a practical example.

Filtering chains by residue count

If you want to select chains with more than 100 residues, simply enter:

To find those with a residue count between 80 and 120:

Selecting leaner chains based on atom count

Large chains slow you down? Only want compact chains? Try:

You can even combine queries to be more selective. For example:

Working with chain segments

Segments help organize chains into meaningful structural stretches (e.g., domains or motifs). To filter chains with more than two segments, use:

Conversely, to find those with exactly one to three segments:

Narrowing down by structural groups

Structural groups are higher-level organizational elements that might contain multiple residues or atoms. You can search for chains that have more than 10 of them:

Or focus on a precise range:

Why this matters

This kind of precise querying can help:

• Filter out chains that are too long or too short for your study.
• Isolate biologically meaningful substructures programmatically.
• Prepare cleaner selections for export, simulation, or visual examination.

No more manual browsing through dozens of chains—the NSL makes this selection process painless and scalable 💡

Want to dig deeper into what attributes are available on chain nodes and how to use them? Check out the full documentation here:
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.