A molecular structure can contain thousands of atoms, but a modeling question is often much narrower: which receptor residues are near the ligand, which contacts involve polar atoms, and which waters might matter? Building each selection manually is easy to get wrong—especially when a task mixes atoms, residues, distance cutoffs, and exclusions.
Node Specification Language (NSL) lets you describe those questions as selections. The examples below form a practical workflow for turning a crowded structure into a focused set of candidates. The expressions are intended to be used in SAMSON’s selection and filtering context.
Start with the region around the ligand
For a first pass, select receptor residues within 6 Å of any ligand, while excluding glycine and alanine:
((n.t r and not r.t GLY,ALA) in n.c rec) w 6A of n.c lig
This is a useful mutagenesis-focused shortlist: it keeps the selection centered on receptor residues near the ligand while applying a residue-type exclusion. The key practical choice is the level of the selection. Here the target is residues (r), not individual atoms. If you instead want the atoms that make up residues in the pocket, use:
n.t a in (n.t r w 5A of n.c lig)
That distinction helps prevent a common workflow mismatch: selecting nearby residues when you need atoms for contact inspection, or selecting only nearby atoms when you need a residue-level list.
Separate contact types instead of using one broad selection
A distance cutoff gives a geometric neighborhood, not a chemical interpretation. After identifying the pocket, make narrower selections for the question you want to investigate. For example, backbone nitrogen atoms within 3 Å of the ligand are selected with:
(a.s N in n.t bb) w 3A of n.c lig
For polar heavy atoms in the receptor within the same distance, use:
(a.s O,N in n.c rec) w 3A of n.c lig
And for ligand heavy atoms—excluding hydrogen atoms—in contact with the receptor within 2 Å:
((n.t a in n.c lig) and not a.s H) w 2A of n.c rec
These selections answer different questions. The first focuses on backbone nitrogens; the second collects receptor oxygen and nitrogen atoms; the third starts from the ligand side and excludes hydrogen atoms. Keeping these distinctions explicit makes the result easier to interpret and share with collaborators.
Check waters and potential clashes
Nearby waters can be worth inspecting separately from the protein. To select water within 4 Å of the ligand, use:
n.c wat w 4A of n.c lig
To look for water oxygens within 3 Å of both receptor and ligand, combine two proximity tests:
(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)
This identifies candidate bridging waters for closer examination; proximity alone does not establish a hydrogen bond or prove that a water is functionally important.
A quick geometric screen for possible steric clashes is ligand heavy atoms within 2.2 Å of receptor heavy atoms:
((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)
Treat this as a way to find close contacts to inspect, rather than a complete energetic assessment.
Use the complement to find what is outside the contact zone
Sometimes the useful result is not the pocket, but what is beyond it. For ligand atoms more than 6 Å from receptor atoms, the examples use:
(n.t a in n.c lig) b 6A of n.c rec
This can help separate a ligand’s contacting region from portions that extend away from the receptor. The examples also use b for selections described as being beyond a cutoff, while w is used for within-distance selections. Check the selection in the context of your structure and task, particularly when combining several conditions.
A small habit that improves selection quality
Build a selection in stages: define the relevant component, choose atoms or residues, add a distance condition, then apply chemical or structural filters. For example, begin with receptor residues near the ligand, narrow to oxygen and nitrogen atoms if the question is about polar contacts, and make a separate water selection rather than folding every component into one expression. This makes it easier to understand why a node was selected and to adjust one criterion without rebuilding the whole query.
For more NSL selection examples and the complete reference table, see the NSL examples documentation.
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