A molecular structure can contain thousands of atoms, but a binding-site question is usually much narrower: Which residues are near the ligand? Are any waters in the pocket? Which atoms might be making close or polar contacts?
Manually selecting each group is slow, and a single selection can mix different levels of detail: atoms, residues, waters, and the ligand itself. SAMSON’s Node Specification Language (NSL) lets you express these questions as readable selections. The key is to build the analysis in layers, starting with a distance shell and then asking more specific questions about its contents.
Start with the residue neighborhood
To find residues within 5 Å of the ligand, use:
n.t r w 5A of n.c lig
This selects nearby residues rather than just the atoms making the closest approach. That can be a more useful first view when you want to inspect the pocket as a collection of amino acids. To expand those residues back into their atoms, use:
n.t a in (n.t r w 5A of n.c lig)
The distinction matters: selecting nearby atoms answers “what is close?”, while selecting residues and then their atoms helps you inspect the full local environment of those residues.
Separate tight contacts from the broader pocket
A 5 Å neighborhood is useful for mapping a site, but it is not the same as a very close contact. To select ligand atoms within 2 Å of receptor atoms, use:
(n.t a in n.c lig) w 2A of n.c rec
For a focused steric-clash screen, the documented example excludes hydrogen atoms on both sides and uses a 2.2 Å cutoff:
((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 gives you a shortlist of close heavy-atom approaches to inspect. Treat it as a geometric screen, not a final verdict: the selection identifies distances, while interpreting their significance requires looking at the molecular context.
Ask what kind of contacts are nearby
To focus on 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
For a more specific view of backbone interactions, select ligand atoms near backbone nitrogen atoms:
(n.t a in n.c lig) w 3A of (a.s N in n.t bb)
These selections narrow the view by atom type and structural role. They can help you examine candidate polar contacts without first scanning every atom in the pocket.
Include waters—but keep them distinct
Water molecules can be important parts of a binding-site environment, so it is useful to inspect them separately from receptor residues. To select waters within 4 Å of the ligand:
n.c wat w 4A of n.c lig
To look for water oxygen atoms 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)
This identifies candidate bridging waters according to the stated distance cutoffs. It does not, by itself, establish whether a water is energetically favorable or should be retained; it gives you a reproducible selection to examine.
A practical way to use these selections
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Begin with residues within 5 Å to outline the local pocket.
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Expand those residues to atoms when you need a fuller structural view.
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Use tighter cutoffs and atom-type filters to investigate close or polar contacts.
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Inspect nearby waters as a separate category, especially when evaluating possible bridges.
Each expression makes its distance threshold and target group explicit. That makes it easier to adjust the cutoff, compare selections, and explain how you produced a shortlist—rather than relying on a manually assembled selection whose rules are difficult to reproduce.
Explore the NSL examples documentation to learn more.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.