A ligand-bound molecular structure can contain thousands of atoms, but a first-pass binding-site question is often simple: which receptor atoms are close enough to matter? The hard part is making the selection precise. Should you select atoms or whole residues? Should waters and hydrogens be included? And how do you separate close contacts from atoms that are definitely outside a chosen distance?
In SAMSON, Node Specification Language (NSL) lets you express these choices as reusable selections. Here is a practical way to think through a small contact-analysis workflow, using examples from the NSL reference.
Start with the question, not the syntax
For a quick view of the binding pocket, select atoms in residues within 5 Å of the ligand:
n.t a in (n.t r w 5A of n.c lig)
This expression has two levels. The inner selection finds residues (r) within 5 Å of the ligand. The outer selection then asks for atoms (a) in those residues. That distinction matters: a residue-level contact can be useful for identifying which parts of the protein line the pocket, while an atom-level selection is more targeted for examining individual interactions.
If the task is specifically to identify receptor atoms close to the ligand, use an atom-level distance selection:
(n.t a in n.c rec) w 5A of n.c lig
The w distance operator selects nodes within the stated distance. Here, the receptor and ligand are identified by their node categories, so the expression is concise and focused on the intended partners.
Make the selection match the analysis
For contact analysis, hydrogens may not be what you want to inspect. To select ligand heavy atoms, the reference combines a ligand atom selection with an explicit hydrogen exclusion:
(n.t a in n.c lig) and not a.s H
You can use the same idea when comparing ligand and receptor heavy atoms for possible steric clashes. This example selects ligand and receptor atoms that are non-hydrogen and within 2.2 Å of one another:
((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 very short distance can help flag close approaches for inspection, but the selection itself is not a diagnosis. It identifies atoms meeting the specified rule; you still need to interpret the structural context.
Keep solvent in—or deliberately leave it out
Water can be relevant to a binding site, so it helps to make its role explicit rather than treating every nearby node as the same kind of contact. To find waters within 4 Å of a ligand, use:
n.c wat w 4A of n.c lig
To find water oxygens close to both receptor and ligand, combine two distance tests:
(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 focuses the selection on oxygen atoms in water that are within 3 Å of each partner. It is a useful starting point for inspecting possible bridging waters, without assuming that every selected water has the same functional role.
Use distance bands to separate near from far
Sometimes the useful question is not simply “what is nearby?” but “what lies in this shell, but not in the inner region?” The reference uses b for nodes beyond a distance. For example, residues within 12 Å of the ligand and beyond 7 Å define a pocket-rim selection:
(n.t r w 12A of n.c lig) and (n.t r b 7A of n.c lig)
Thinking in distance bands can help organize an inspection: a close-contact region, a surrounding shell, and more distant structure. The thresholds should follow the question you are investigating; the expressions make those cutoffs visible and easy to revise.
A practical habit: read selections from the inside out
When an expression becomes long, identify its parts before using it. First locate the object being selected (atoms, residues, waters, or another node type). Then check the category or property filters, such as receptor membership or element. Finally, read each distance condition and confirm which two groups are being compared. Parentheses help make these relationships explicit.
This approach also makes it easier to adapt a selection safely. For example, you can change a 5 Å pocket neighborhood to 4 Å, or add an exclusion, while keeping the underlying question intact. NSL expressions are most useful when their structure reflects the biological question rather than merely being copied as a string.
Explore more selection patterns in the NSL examples documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.