Easily Find the Right Atoms in Your Molecule Using NSL and the Find Command

If you’ve ever found yourself tediously clicking through atoms, residues, or chains to isolate just the right part of your molecule, you’re not alone. Molecule modelers often face the task of selecting specific parts of complex structures—be it a ligand, a chain, or atoms with certain properties. This process can become especially time-consuming in large biomolecular systems. Fortunately, SAMSON’s Node Specification Language (NSL) combined with the Find command offers a much faster and more precise way to handle these situations.

The Find command in SAMSON lets you enter NSL expressions to instantly select specific nodes in your document. Whether you want all atoms of a certain type, residues in specific ID ranges, or structures near a certain residue, NSL has you covered with concise syntax and powerful filtering.

Getting Started: How to Use the Find Command

To access the Find command in SAMSON, go to the top-left corner of the interface and look for the Find search bar. Once it’s active, you can type NSL expressions to specify what you want to select.

Select nodes with the Find command

For example, entering "ALA (with the starting quote only) followed by pressing the Tab key displays auto-completion suggestions like the following:

  • "ALA 22 Backbone"
  • "ALA 22 Side chain"
  • "ALA 28"

This is particularly useful when searching by residue name, or if you only remember part of a structure’s name.

Make More Powerful Selections

Here are some example NSL expressions for quick reference:

  • n.c lig, rec: Selects all ligands and receptors
  • r.id 20:40: Matches residues with IDs between 20 and 40
  • H: Selects all hydrogen atoms
  • C in n.s: Selects carbon atoms within the current selection

Let the AI Assistant Help

Not sure which NSL expression to use? Let the AI Assistant lend a hand. Simply click the Ask AI button (Ask AI) next to the selection field, and describe what you want. The Assistant understands the document structure and can generate the appropriate NSL string for you.

Use Cases: Real-World Scenarios

NSL expressions can help with various typical workflows:

  • Drilling down into a specific side chain: n.t sc and r.t LYS helps you see only side chains of lysines.
  • Looking at atoms in a chain ID range: a.ci > 2 filters atoms from chain IDs greater than 2.
  • Selecting all alpha helices: r.ss h limits your view to helices only.

Whether you’re prepping for simulations or editing a molecular system, NSL saves time and precision matters. Once you get used to the powerful, flexible syntax, it’s hard to go back to manual selection.

To learn more about NSL and how to use it in other parts of the interface such as the Document view, visit the official NSL documentation.

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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