A molecular structure can contain thousands of atoms, but a binding-site question is often much narrower: Which receptor atoms touch the ligand? Are nearby waters involved? Which residues are close enough to inspect, and which contacts might be unusually tight?
Building each selection from scratch can be tedious—and it is easy to confuse a residue-level neighborhood with an atom-level contact. In SAMSON, Node Specification Language (NSL) lets you express these questions as readable selections. The examples below form a practical starting point for inspecting a ligand pocket. Distances are in angstroms (Å); the cutoff you choose determines what counts as “near,” not whether an interaction is energetically favorable.
Start with the atoms that actually contact the ligand
For a contact map, first select receptor atoms within 5 Å of the ligand:
(n.t a in n.c rec) w 5A of n.c lig
This expression narrows the selection in two steps: n.t a in n.c rec specifies receptor atoms, and w 5A of n.c lig selects those within 5 Å of ligand nodes. If you want the nearby residues instead of individual atoms, change the selected node type:
(n.t r and not r.t GLY,ALA) in n.c rec w 6A of n.c lig
The documented example combines the residue selection with an exclusion for glycine and alanine. Its purpose is different from the atom selection: it helps focus a residue-level inspection, rather than listing every contacting atom. Parentheses make the intended grouping easier to read. When adapting a query, preserve the scope of each condition and check whether you mean atoms (a) or residues (r).
Separate heavy-atom contacts from possible clashes
Hydrogens can make an atom-level contact selection busier. For ligand heavy atoms, exclude hydrogen explicitly:
(n.t a in n.c lig) and not a.s H
To select close contacts between ligand and receptor heavy atoms, use a narrower cutoff:
((n.t a in n.c lig) and not a.s H) w 2.2A of ((n.t a in n.c rec) and not a.s H)
This is a useful way to flag possible steric clashes for visual review. Treat it as a distance-based screen: the selection identifies atom pairs meeting the cutoff, but does not by itself establish that a clash is chemically meaningful or diagnose its cause.
Check polar contacts and waters separately
To focus on receptor oxygen and nitrogen atoms close to the ligand, use:
(a.s O,N in n.c rec) w 3A of n.c lig
For waters that may sit between receptor and ligand, the examples include a selection of water oxygens within 3 Å of both:
(a.s O in n.c wat) and (n.t a w 3A of n.c rec) and (n.t a w 3A of n.c lig)
Looking at these selections separately can make an inspection more informative: one highlights nearby polar atoms, while the other asks whether water oxygen atoms are close to both molecular components. A nearby water is a candidate to examine, not proof of a bridging interaction.
Use a sequence of questions, not one giant query
- Map the neighborhood: select receptor residues within 5 Å of the ligand.
- Inspect the atom contacts: select receptor atoms, or restrict the selection to oxygen and nitrogen atoms.
- Review solvent: select nearby waters and, if useful, water oxygens close to both partners.
- Flag tight contacts: apply a smaller cutoff to heavy atoms and inspect the resulting pairs in context.
This staged approach makes it easier to understand what each result represents and adjust one question at a time. A 3 Å selection and a 5 Å selection answer different practical questions; neither is a universal boundary for all interactions. The NSL examples page includes additional patterns for chain-specific interfaces, aromatic residues, charged residues, metals, glycans, and more.
Explore the original NSL examples documentation to adapt these selections to your structure and analysis goals.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.