From a crowded structure to a useful contact map

A molecular structure can contain thousands of atoms, but a modeling question is often much narrower: Which receptor residues are close to the ligand? Are nearby waters part of the interaction network? Which contacts are tight enough to inspect as possible clashes?

Building those selections by hand is tedious, and broad selections can hide the difference between atoms, residues, and whole molecular components. SAMSON’s Node Specification Language (NSL) lets you describe the target and the spatial relationship together. The examples below form a practical starting point for mapping a binding site and checking what is around it.

Start with the question, not the whole structure

For a first-pass binding-site selection, select atoms belonging to residues within 5 Å of the ligand:

This expression has two steps. n.t r w 5A of n.c lig identifies residues within the specified distance of the ligand. The outer n.t a in then selects the atoms in those residues. That distinction matters: a residue-level selection is useful for listing or comparing residues, while an atom-level selection is more useful when you want to inspect individual contacts.

If you want only receptor atoms close to the ligand, use:

The first condition limits the candidates to receptor atoms; the second applies the distance test. Combining those filters makes the intent explicit and helps avoid accidentally including ligand, water, or other atoms in the result.

Separate direct contacts from the surrounding environment

Distance cutoffs are not interchangeable: choose one that matches the question you are asking, then inspect the resulting selection in context. For a tight-contact check, select ligand atoms within 2 Å of receptor atoms:

For a broader view of ligand-adjacent receptor atoms, increase the cutoff, for example to 5 Å. A broader shell can help you see the pocket’s chemical surroundings, while a tighter cutoff focuses attention on close approaches. Neither selection by itself establishes whether a contact is favorable or unfavorable; it identifies geometry to investigate.

To focus on non-hydrogen atoms when screening for steric clashes, use the documented 2.2 Å example:

Filtering both sides to exclude hydrogen atoms keeps the comparison focused on heavy atoms. The result is a candidate set for inspection, not a substitute for evaluating the model, its preparation, or the interaction energetics.

Ask whether water is part of the story

Waters can be easy to overlook when a selection includes only receptor and ligand. To find waters within 4 Å of the ligand, use:

You can also look for water oxygens within 3 Å of both receptor and ligand:

This is a way to identify candidate bridging waters for closer review. It does not determine whether a water is structurally conserved or energetically important, but it narrows the inspection to waters that satisfy both distance conditions.

Make selections easier to reason about

A useful habit is to build a selection in layers: first choose the node type or component, then add the spatial cutoff, and finally add chemical or structural constraints. For example, polar oxygen and nitrogen atoms in the receptor within 3 Å of the ligand are selected with:

For aromatic-residue candidates within 5 Å, the expression is:

These examples show how NSL can combine atom or residue identity, component membership, and spatial relationships in a readable expression. When adapting them, confirm that the structure’s components are classified as expected (for example, ligand, receptor, and water), and check whether your question calls for atoms or residues. A clear selection is easier to reproduce, explain to collaborators, and revisit when comparing models.

For more selection patterns and the full set of examples, see the NSL examples documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.