A molecular structure can contain several chains, and it is easy to lose time inspecting them one by one. One chain may be the protein of interest; others may be shorter, longer, or simply have different chain IDs. SAMSON’s Node Specification Language (NSL) lets you describe chain-level criteria directly, so you can narrow the search by identity, residue count, or other properties.
The key distinction is that the chain attribute space matches chain nodes only. Its short form is c. That means a query such as c.id 2 is about chains with chain ID 2—not about individual atoms or residues.
Start with chain identity
If a structure uses chain IDs and you know which one you need, filter by ID:
c.id 1matches chains whose chain ID is 1.c.id <= 3matches chains with an ID no greater than 3.c.id 2:4, 6matches IDs 2 through 4, as well as ID 6.
This is a useful first pass when a structure has several chains and you want to focus on a known chain or a small group of IDs. If you are unsure which ID corresponds to the molecule you need, use size as another clue rather than relying on the ID alone.
Use residue count to narrow by size
The number of residues is often a practical way to distinguish a long chain from a shorter one. The full attribute is chain.numberOfResidues; its short form is c.nr.
c.nr > 100matches chains with more than 100 residues.c.nr 100:120matches chains with a residue count between 100 and 120.
For example, if you are looking for a chain above a particular size threshold, the first expression gives you a concise criterion. If you have an expected size range, the second makes that range explicit. These queries help reduce the candidate set; they do not, by themselves, establish what a chain’s biological role is.
Check segments and structural groups
When residue count is not enough to distinguish the chains you are comparing, NSL also provides chain-level counts for segments and structural groups:
c.ns > 2matches chains with more than two segments.c.ns 2:4matches chains with between two and four segments.c.nsg > 10matches chains with more than ten structural groups.c.nsg 10:12matches chains with between ten and twelve structural groups.
These are separate attributes, so choose the one that reflects the information you actually have. Residue count, segment count, and structural-group count describe different properties; a result that fits one criterion may not fit another.
Combine the reference with inherited attributes
Chain nodes also inherit attributes from the node and structural-group spaces. For example, a chain can be matched by its name with c.n "A", or by a number of atoms with c.nat < 1000. The reference lists additional inherited properties, including elemental counts and charge. This makes the chain attribute space useful for more than chain IDs alone.
A simple way to approach an unfamiliar structure is to begin with the most reliable fact you know—often an ID or approximate residue count—then refine your search using another documented property. Keep the expressions readable, and check that each criterion refers to the intended level of the structure: these chain attributes describe chains, not individual residues.
For the complete list of chain attributes, short names, and examples, see the SAMSON chain NSL reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.