A molecular structure can make a binding site look deceptively simple: there is a ligand, a surrounding protein, perhaps a few waters—and many thousands of atoms that are not relevant to the question at hand. The practical challenge is to turn “show me what is near the ligand” into a selection that is specific enough to interpret, while avoiding common distractions such as hydrogens, solvent, or residues outside the receptor.
In SAMSON, Node Specification Language (NSL) lets you express these criteria as reusable selections. The examples below form a small workflow for exploring a ligand’s neighborhood. They are useful when preparing a contact analysis, inspecting a pocket, or narrowing a structure before asking a more detailed question.
Start with the receptor residues around the ligand
To select receptor residues within 6 Å of the ligand, while excluding glycine and alanine, use:
((n.t r and not r.t GLY,ALA) in n.c rec) w 6A of n.c lig
This expression combines several filters: it targets residues (r), excludes the two named residue types, limits the selection to the receptor, and then applies a distance criterion relative to the ligand. Combining these conditions is more useful than selecting every node near the ligand: the result is already focused on receptor residues relevant to the pocket.
If you want to inspect the pocket as atoms rather than residues, select atoms belonging to residues within 5 Å:
n.t a in (n.t r w 5A of n.c lig)
The order matters conceptually: first identify nearby residues, then select their atoms. This gives you the atoms of the surrounding residues, not just the atoms that happen to fall within 5 Å themselves.
Choose the atoms that answer your question
For a contact-focused view, it can help to isolate a particular chemical group. 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
That is narrower than selecting every atom in the nearby residues. It can help when you are examining possible close approaches involving backbone nitrogens. For a broader ligand-side selection, this expression selects ligand heavy atoms:
(n.t a in n.c lig) and not a.s H
Separating the ligand atoms from the surrounding receptor atoms can make it easier to inspect which side of a contact you are considering. The same idea supports a simple clash-focused selection: 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)
This is a distance-based way to flag very close heavy-atom pairs for inspection. Treat it as a selection to investigate, rather than as an automatic verdict about whether a structure is wrong.
Keep waters in—or deliberately leave them out
Waters can be important to a binding-site interpretation, but including every water in every selection can make a view harder to read. To select waters within 4 Å of the ligand, use:
n.c wat w 4A of n.c lig
To focus instead on receptor atoms within 5 Å of the ligand but more than 3 Å from water oxygens, use:
(n.t a in n.c rec) and (n.t a w 5A of n.c lig) and (n.t a b 3A of (a.s O in n.c wat))
Here, w expresses a within-distance condition and b is used for the beyond-distance condition in the examples. Together, they help distinguish a ligand-adjacent receptor atom from one that is also close to a water oxygen. That distinction can be useful when comparing a dry-looking pocket region with one where solvent may contribute to the local environment.
Build selections in layers
A reliable way to work with complex selections is to begin with the biological object you care about—such as the receptor or ligand—then add the node type, chemistry, and distance filters. Check that each part reflects the question you intend to ask. “Nearby residues,” “nearby atoms,” and “atoms in nearby residues” are not interchangeable, and choosing the right level can prevent a selection from being broader or narrower than expected.
These expressions are starting points, not universal definitions of a binding site. The useful cutoff depends on the analysis, and the structure’s available annotations determine which categories can be selected. Still, keeping the selection logic explicit makes it easier to revise a cutoff, include waters, or focus on a specific atom type without rebuilding the query from scratch.
For more NSL selection examples, see the NSL examples documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.