A molecular structure can contain thousands of atoms, but a binding-site question is often much narrower: which receptor residues are near the ligand, which atoms make close contacts, and which nearby waters might matter? Manually building these selections is tedious—and small changes in what you select can change the answer.
SAMSON’s Node Specification Language (NSL) lets you describe the selection in terms of molecular features and distance relationships. The key is to make the question explicit: choose the kind of node you want (such as atoms or residues), define the molecular group, and then apply a distance criterion.
Start with residues, not every atom
For a first pass at the binding pocket, select receptor residues within 5 Å of the ligand:
(n.t r w 5A of n.c lig)
This is a useful shortlist when your next step is to inspect the pocket as a set of residues. If you instead need the atoms belonging to residues in that shortlist, express that extra step directly:
n.t a in (n.t r w 5A of n.c lig)
The distinction matters. The first expression targets nearby residues; the second targets atoms inside those nearby residues. In practice, selecting at the level that matches your analysis can make results easier to interpret.
Refine the shortlist for a specific question
A distance-only selection can include residues you do not want to investigate. To focus on receptor residues 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 is an example of combining three ideas: restrict the selection to residues, specify the receptor, and exclude particular residue types before applying the distance criterion. It can be useful when the goal is to focus a mutagenesis shortlist, rather than simply map everything nearby.
For a more chemically specific view, select polar oxygen and nitrogen atoms in the receptor that are within 3 Å of the ligand:
(a.s O,N in n.c rec) w 3A of n.c lig
Or identify ligand heavy atoms close to receptor atoms—a useful way to review tight contacts—by selecting ligand atoms, excluding hydrogen, and setting a 2 Å distance:
(n.t a in n.c lig) w 2A of n.c rec
These expressions answer different questions: one finds polar receptor atoms near the ligand; the other finds ligand atoms near the receptor. Keeping track of which side of a contact is being selected helps avoid misreading the result.
Separate pocket contacts from nearby waters
Water molecules can be important parts of a binding site, but they are often worth examining separately from protein residues. To select waters within 4 Å of the ligand:
n.c wat w 4A of n.c lig
To find water oxygens that are within 3 Å of both receptor and ligand, combine two distance conditions:
(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 gives you a targeted selection for reviewing possible bridging waters. It does not, by itself, establish that a water is energetically important or that it should be retained; it helps identify candidates for further inspection.
Use distance bands to explore the pocket edge
Not every useful residue is in direct contact with a ligand. To examine a surrounding shell between 7 and 12 Å, select residues within 12 Å and exclude those within 7 Å:
(n.t r w 12A of n.c lig) and (n.t r b 7A of n.c lig)
That broader shell can help distinguish the immediate pocket from the surrounding environment. More generally, build selections in small, readable steps: choose the node type, specify the relevant component or chemistry, then add distance and exclusion conditions. This makes it easier to see what a selection is intended to capture and to adapt it when the scientific question changes.
For more NSL selection examples, see the NSL examples documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.