A molecular structure can contain thousands of atoms, but a useful binding-site question is often much smaller: Which receptor residues are near the ligand? Which contacts involve polar atoms? Are nearby waters or possible clashes worth inspecting? Finding these atoms one by one is tedious, and a single broad selection can hide the chemical detail you need.
In SAMSON, Node Specification Language (NSL) lets you describe the selection in terms of structural features and distance relationships. The expressions below turn common binding-site checks into reusable queries. They are examples to adapt to the names and contents of your own structure—not a substitute for checking that the selected nodes match your intended analysis.
Start with a distance-defined pocket
For a quick view of the binding environment, select atoms belonging to residues within 5 Å of the ligand:
n.t a in (n.t r w 5A of n.c lig)
This expression first identifies residues near the ligand, then selects their atoms. That distinction matters: selecting atoms near a ligand and selecting all atoms in nearby residues are different tasks. The first focuses on direct proximity; the second gives you the surrounding residue context.
If you want the residues themselves rather than their atoms, use:
n.t r w 5A of n.c lig
For receptor-only results, add the receptor category:
((n.t r in n.c rec) w 5A of n.c lig)
Make the selection chemically informative
A pocket shortlist becomes more useful when you narrow it by chemistry. To find polar oxygen and nitrogen atoms in the receptor within 3 Å of the ligand, use:
(a.s O,N in n.c rec) w 3A of n.c lig
To focus on aromatic residue candidates within 5 Å, use:
(r.t PHE,TYR,TRP,HIS) and (n.t r w 5A of n.c lig)
Or inspect positive receptor residues close to the ligand:
(r.c positive in n.c rec) w 4A of n.c lig
These selections help separate different questions—polar proximity, aromatic environment, and charge—from the general shape of the pocket. They identify candidates by the properties encoded in the structure; they do not, by themselves, establish that a hydrogen bond, stacking interaction, or salt bridge is energetically favorable.
Check water and steric proximity separately
Waters can be important to inspect rather than automatically treating them as part of the receptor. To select water nodes within 4 Å of the ligand, use:
n.c wat w 4A of n.c lig
For a tighter steric-clash screen, compare ligand and receptor heavy atoms within 2.2 Å:
((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)
A short distance is a flag for review, not a diagnosis on its own. Check atom identities, alternate locations, occupancy, and the structural context before deciding whether a contact represents a clash or an issue with the input model.
Build selections in layers
A practical way to avoid overly complicated queries is to work from broad to specific: select nearby residues, restrict them to the receptor, then apply atom or chemical filters. For example, receptor residues near the ligand that are not glycine or alanine can be expressed as:
((n.t r and not r.t GLY,ALA) in n.c rec) w 6A of n.c lig
For residues close to the ligand but beyond 7 Å—useful when you want a surrounding shell rather than the immediate pocket—the documented pattern is:
(n.t r w 12A of n.c lig) and (n.t r b 7A of n.c lig)
Distance cutoffs are choices, not universal boundaries. Compare a few sensible ranges and inspect the resulting selection in the structure. Also make sure categories such as ligand, receptor, and water correspond to the nodes in your model; a correct-looking expression cannot compensate for an incorrectly classified structure.
These examples make it easier to turn a vague question—“what is around this ligand?”—into a specific, inspectable selection. For more NSL examples and related syntax, see the SAMSON NSL examples reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.