Finding Exactly the Atoms You Want: Using Atom Attributes in NSL

When working with large molecular systems, identifying specific atoms with precision can be time-consuming and frustrating. Whether you’re cleaning up a model, extracting meaningful subsets, or analyzing specific substructures, selecting atoms by hand becomes inefficient and error-prone very quickly.

This is where the Node Specification Language (NSL) in SAMSON can save hours of manual work. NSL enables precise, attribute-based filtering of atoms using a powerful and concise query language. SAMSON’s NSL offers dozens of atom attributes you can use to define filters tailored exactly to the atoms you need.

Why Attribute-Based Filtering Matters

Let’s imagine you want to:

  • Identify all aromatic carbon atoms.
  • Select atoms within a certain residue range in chain B.
  • Extract polar hydrogens involved in hydrogen bonds.

You’ll need a flexible way to combine geometric, chemical, and structural criteria. The atom attribute space (short name a) makes queries like these possible in just a few characters.

A Look at Common Atom Attributes

Here are just a few examples of how attributes are used inside NSL:

  • a.ar: matches aromatic atoms
  • a.s C: matches atoms with symbol C (carbon)
  • a.c B: atoms from chain B
  • a.resi 40:60: residue sequence numbers between 40 and 60

For instance, to select aromatic carbon atoms, simply use:

a.s C and a.ar

Combining Atom Attributes

Atom attributes can be combined using logical operators like and, or, and not. This gives you expressive control over your selection criteria. Consider these examples:

  • a.s O and a.w: selects oxygen atoms flagged as water
  • a.ar and not a.pl: selects aromatic atoms that are not planar
  • a.hbd and a.hba: finds atoms that are both hydrogen bond donors and acceptors

Going Further: Geometric and Electronic Attributes

If you’re dealing with specific molecular properties or simulations, NSL also offers attributes like:

  • a.pc: partial charge
  • a.hy: hybridization (e.g., sp2)
  • a.tf: B-factor / temperature factor
  • a.g: geometry (e.g., tetrahedral)

A more complex example: select all planar nitrogen atoms with a partial charge over 1:

a.s N and a.pl and a.pc > 1

Tips for Efficient Use

  • Use short names: a.s, a.pc, a.g, etc. make queries faster to write.
  • Chain filters using and/or – no need to click through visual interfaces.
  • Combine with node types (e.g., n.t a and not a.met): this excludes metallic atoms.

Your Workflow Streamlined

Atom attribute filters are indispensable whether you’re:

  • Preprocessing structures for simulations
  • Extracting functional groups
  • Comparing structural motifs
  • Building custom selection rules for scripts

The more comfortable you become with NSL, the less you’ll find yourself reaching for manual selection tools. Learning just a handful of these attributes can save hours and foster more repeatable, reliable modeling workflows.

To learn more and explore the full list of available attributes, visit the documentation page: https://documentation.samson-connect.net/users/latest/nsl/atom/

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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