A molecular structure can contain far more than the atoms you need to inspect: solvent, ions, glycans, alternate conformations, and residues far from the binding site. The challenge is not simply finding atoms near a ligand. It is making a selection that answers a specific question, then refining it without losing track of what the selection means.
SAMSON’s Node Specification Language (NSL) lets you express these questions as selections. A practical starting point is to identify receptor residues close to a ligand, then choose whether you need whole residues, individual atoms, or a particular chemical subset. The examples below show how to build that shortlist and investigate it from several angles.
Start with nearby residues
To find receptor residues within 5 Å of a ligand, use:
(n.t r w 5A of n.c lig) and (n.t r in n.c rec)
The first part specifies the distance relationship; the second restricts the result to receptor residues. Keeping these conditions visible is useful: it makes clear both where the selection is and what kind of structure it includes. For a residue-level view, this is often more useful than starting with every atom in the structure.
If you want the atoms belonging to nearby residues, select atoms in the residue selection:
n.t a in (n.t r w 5A of n.c lig)
This distinction matters when preparing a view or analysis. A residue-level selection helps identify which amino acids line the pocket; an atom-level selection is more targeted for inspecting contacts or geometry.
Separate direct contacts from the surrounding pocket
A 5 Å neighborhood is a useful way to define a pocket region, but it is not the same as a tight contact. For example, the documentation gives this expression for ligand atoms within 2 Å of receptor atoms:
(n.t a in n.c lig) w 2A of n.c rec
For a stricter steric-clash shortlist, the example uses a 2.2 Å cutoff and excludes hydrogen atoms on both sides:
((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)
These selections answer different questions. A broader neighborhood helps map the pocket; a very short heavy-atom separation flags close approaches worth checking. Treat the distance as a filter for inspection, not as a verdict about whether a structure is wrong.
Check whether waters are part of the picture
Water can be relevant to a binding-site interpretation, so it can help to examine it separately from the protein. This expression selects water within 4 Å of any ligand:
n.c wat w 4A of n.c lig
To find water oxygens positioned within 3 Å of both receptor and ligand, use:
(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)
The latter is a focused way to look for possible bridging waters. It does not, by itself, establish that a water forms a functional bridge; it identifies candidates by atom type and distance so you can inspect them in context.
Refine the shortlist by chemistry
Once you have a spatial region, NSL can narrow it by residue or atom properties. For example, aromatic residues within 5 Å of the ligand can be selected with:
(r.t PHE,TYR,TRP,HIS) and (n.t r w 5A of n.c lig)
To focus on polar oxygen and nitrogen atoms in the receptor within 3 Å, use:
(a.s O,N in n.c rec) w 3A of n.c lig
These filters make the selection more interpretable: instead of looking at every nearby atom, you can ask which aromatic residues or polar atoms are close enough to merit attention. The same general pattern works throughout the examples: define a structural category, apply a distance condition, and add exclusions or additional properties only when they serve the question.
A small workflow for clearer selections
- Choose the target level. Decide whether the question concerns residues, atoms, or a specific atom subset.
- Set a distance that matches the question. A pocket neighborhood and a tight-contact screen are not interchangeable.
- Limit the structural category. Use receptor, ligand, or water conditions to avoid mixing unrelated components.
- Add chemical filters. Narrow the result to atom types or residue types relevant to the interaction you are investigating.
- Inspect the result in context. A selection identifies candidates; interpretation still depends on the surrounding structure and the purpose of the analysis.
Thinking in these steps turns a long selection expression into a sequence of understandable decisions. It also makes it easier to adapt the selection when the question changes—for example, from mapping a pocket to checking polar contacts or locating nearby waters.
For more NSL selection examples, see the SAMSON NSL examples reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.