When a molecular structure contains many residues, finding the side chains relevant to a particular question can become a small but persistent bottleneck. You may want to inspect side chains with a certain atom count, compare groups by elemental composition, or locate candidates with a particular charge. Clicking through the structure one residue at a time makes those searches harder to repeat and easier to get wrong.
SAMSON’s Node Specification Language (NSL) lets you describe side-chain searches through attributes. The side-chain attribute space is called sideChain, and the documentation examples use the prefix sc. A useful way to approach a search is to start with one measurable property, check whether the result is sensible, and then refine the criterion.
Start with a count, not a guess
Atom-count attributes are useful when you need to narrow a large set without relying on residue names. For example, sc.nat < 1000 selects side chains with fewer than 1,000 atoms, while sc.nat 100:200 specifies a range. Element-specific counts work in the same style: sc.nC < 10 checks the number of carbons, and sc.nO 10:20 specifies a range of oxygens.
These examples are deliberately broad. Their practical value is that they show the shape of the query: choose the attribute that corresponds to the property you need, then choose a comparison or interval appropriate to your structure. A threshold that is useful for one model may be unhelpful for another, so treat the numbers as examples rather than universal cutoffs.
Use composition to make a search more specific
NSL provides counts for carbon, hydrogen, nitrogen, oxygen, sulfur, and coarse-grained atoms. That can help turn a vague inspection task into a reproducible criterion. For instance, if you are reviewing side chains with a particular oxygen-count range, you can express that directly with sc.nO 10:20. If you are comparing atom counts, sc.nH < 10 and sc.nN 10:20 illustrate the corresponding hydrogen and nitrogen attributes.
Formal charge and partial charge offer another way to describe candidates. The examples include sc.fc > 1 and sc.fc 6:8 for formal charge, and sc.pc > 1.5 or sc.pc 1.5:2.0 for partial charge. Formal charge uses integer values; partial charge uses floating-point values. Keeping that distinction in mind helps you choose a meaningful comparison and avoid treating the two attributes as interchangeable.
Check identity and visibility separately
Composition is not always the question. Side chains inherit node attributes such as name, visible, and selected. Name examples include sc.n "A" and sc.n "L*"; visibility can be expressed as sc.v or not sc.v. Selection is written as sc.selected or not sc.selected. One detail worth remembering: the documentation says selected does not have the short name s, so use the full attribute name in that expression.
For a reliable workflow, write down the property you are screening for, choose its matching attribute, and try the documented expression on its own. Review the matches before changing the threshold. This makes it easier to spot a query that is too broad or too narrow, and it leaves you with a search you can reuse instead of an undocumented sequence of manual selections.
For the complete attribute reference and additional examples, see the SAMSON side-chain attributes documentation.
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