Quickly Find Segments by Atom, Residue, or Charge Counts in SAMSON

When working with complex molecular systems, molecular modelers often face a recurring challenge: filtering and selecting specific parts of large biomolecules for focused analysis or operations. Whether you’re interested in molecules with a high partial charge, specific atomic compositions, or segments containing a certain number of residues, isolating the right components quickly can save you significant time.

This is where the Segment attribute space in the Node Specification Language (NSL) of SAMSON becomes a powerful solution. Understanding how to use segment attributes can help you go from manually navigating large structures to writing simple, precise queries that select exactly what you need.

What Are Segment Attributes?

The segment attribute space (short name: s) is a focused way to query segment nodes in SAMSON. These segments may correspond to domains or chains in biomolecules, and they play a key role in large system representations.

You can use segment attributes to search based on:

  • Visibility and selection states (s.selected, s.v)
  • Charge values (s.fc, s.pc)
  • Atoms and element counts (e.g., s.nC for carbon atoms)
  • Structure complexity (s.nr for residue count, s.nsg for structural groups)

Examples That Save Time

Here are a few practical use cases:

  • Want to select segments with many residues? Try: s.nr > 130
  • Looking for candidates for coarse-grained modeling? Use: s.ncga > 500
  • Investigating high partial charges? Type: s.pc > 1.5
  • Filtering segments with a high number of carbon atoms? Use: s.nC > 15
  • Focusing on segments rich in nitrogen and sulfur? Combine: s.nN > 10 and s.nS > 5

Making Segment Queries Easier with Short Names

One of the advantages of the NSL is its use of short names to make queries both shorter and easier to read. Here’s a quick mapping of helpful short names:

  • fc: formalCharge
  • pc: partialCharge
  • nr: numberOfResidues
  • nC, nH, nN, nO, nS: numberOf[Element]

Combine these for compact, powerful queries such as:

s.nr 100:150 and s.pc > 1.2 and s.v – selects visible segments containing between 100 and 150 residues and a partial charge above 1.2.

Why It Matters

When developing and testing molecular models, especially for simulations or coarse-grained representations, being able to focus attention on specific types of molecular segments becomes critical. Segment filters not only streamline workflows but also reduce human error in selection and preparation steps.

Learn more about segment attributes and how to use them in advanced selections in SAMSON at the official documentation.

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

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