When a molecular structure contains many residues, finding the side chains relevant to a question can become a small but persistent chore. You might be looking for groups with a particular atom composition, a charge value, or simply a residue name. In SAMSON, the side-chain attribute space in the Node Specification Language (NSL) lets you express these kinds of filters directly, rather than relying only on visual inspection.
Start with the side-chain namespace
Side-chain attributes use the sideChain attribute space, whose short name is sc. A query beginning with sc. therefore targets side-chain nodes. That scope matters: it helps keep a filter focused on the molecular groups you intend to inspect, rather than applying the same criterion to every kind of node.
For example, a side chain with fewer than ten carbon atoms can be specified as sc.nC < 10. The shorter name nC represents numberOfCarbons. For a range, the documented form is sc.nC 10:20. Similar count attributes are available for atoms overall (nat), hydrogens (nH), nitrogens (nN), oxygens (nO), and sulfurs (nS).
Use composition to narrow a search
Composition is useful when a residue name is not the most convenient way to describe what you are seeking. You can use a single count to make a broad first pass—for example, sc.nO > 0 describes a threshold on the number of oxygens—or use the documented range form, such as sc.nO 10:20, when that interval is relevant. The same pattern applies to the other atom-count attributes.
For a size-oriented filter, sc.nat < 1000 checks the total atom count, while sc.ncga 100:200 uses the number of coarse-grained atoms. These attributes let you describe a group by measurable properties instead of having to remember every possible name. The useful threshold or interval depends on the structure and the question, so treat the values as criteria to adapt—not universal cutoffs.
Keep charge criteria distinct
The side-chain attribute space includes both formalCharge (fc) and partialCharge (pc). They are separate attributes, so choose the one that matches the quantity you mean to inspect. The documentation demonstrates integer comparisons and ranges for formal charge, such as sc.fc > 1 and sc.fc 6:8, and floating-point comparisons and ranges for partial charge, such as sc.pc > 1.5 and sc.pc 1.5:2.0.
This distinction is especially useful when translating a scientific question into a search: write down whether you mean formal charge or partial charge before choosing the attribute. A query can only be as clear as the property it expresses.
Use names and state when they are the right criteria
If you already know the name pattern you want, use sc.n, the short name for name. The reference includes examples such as sc.n "A" and sc.n "L*". For visual or selection state, side chains inherit node attributes: sc.v checks visibility, and sc.selected checks selection. You can negate the documented Boolean examples with expressions such as not sc.v or not sc.selected.
One small syntax detail is easy to miss: selected has no short name in this attribute space. Use sc.selected, not a guessed abbreviation. Other Boolean attributes include sc.h for hidden, sc.hm for hasMaterial, sc.om for ownsMaterial, and sc.vf and sc.sf for visibility and selection flags.
A practical way to build a filter
Begin with the question you need answered: name, composition, charge, or display state. Pick the matching attribute, then use a comparison or range that reflects your actual cutoff. Check that the expression begins in the side-chain namespace, and remember that these properties are inherited from broader node or structural-group attribute spaces. This approach makes it easier to understand what a query is testing—and to revise it when your selection is too broad or too narrow.
For the complete attribute list and syntax examples, see the SAMSON side-chain attribute reference.
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