When a molecular model contains many residues, finding the side chains relevant to a question can become a tedious visual scan. Maybe you want to inspect sulfur-containing groups, narrow attention to side chains with a certain number of atoms, or check charge-related properties. In SAMSON, the Node Specification Language (NSL) lets you describe these criteria with compact expressions.
This guide focuses on a practical starting point: filtering side-chain nodes by their composition and charge attributes. The key is to use the sc attribute-space prefix. It identifies the side-chain attribute space, so the expression says not just what property to test, but which kind of node to test it on.
Start with the question, then choose an attribute
For composition, the side-chain attributes include counts of atoms and selected elements:
sc.nat— number of atomssc.nC— number of carbonssc.nH— number of hydrogenssc.nN— number of nitrogenssc.nO— number of oxygenssc.nS— number of sulfurssc.ncga— number of coarse-grained atoms
These attributes take integer values. That makes them useful when a visual impression is too vague: instead of scanning structures and guessing which side chains are larger, you can specify a count or a range. For example, sc.nC < 10 selects side chains with fewer than ten carbons, while sc.nC 10:20 expresses a range. The documentation also gives sc.nat < 1000 and sc.nat 100:200 as examples for total atom counts.
Element counts can help turn a broad inspection into a more focused one. If your question concerns sulfur content, start with sc.nS; for nitrogen or oxygen counts, use sc.nN or sc.nO. The available examples show how to compare counts to a threshold or provide a range, such as sc.nO < 10 or sc.nO 10:20. Treat these as selection criteria—not as a substitute for interpreting the chemistry of the resulting structure.
Keep formal and partial charge distinct
Charge-related searches offer two different attributes. sc.fc is formal charge and accepts integer comparisons or ranges; the documented examples include sc.fc > 1 and sc.fc 6:8. sc.pc is partial charge and accepts floating-point values, with examples such as sc.pc > 1.5 and sc.pc 1.5:2.0.
That distinction matters when translating a scientific question into a query. Formal charge and partial charge are separate properties in NSL, so choose the one that matches the quantity you intend to examine. The expressions above show the syntax; they do not, by themselves, establish what a particular charge value means for your model.
Don’t confuse the node prefix with a property
Side-chain attributes inherit some properties from other attribute spaces. For example, sc.selected tests selection state, and sc.v refers to visibility. Although the side-chain space is abbreviated as s, the documentation specifically notes that selected has no short name there. Using the explicit form sc.selected avoids confusing the side-chain prefix with a shortened attribute.
A simple workflow is to write down the property you care about, choose the matching attribute, and then express the threshold or range using the examples as a syntax guide. Start with one criterion at a time; that makes it easier to see whether the selection matches your intent before making the search more specific.
For the complete attribute list and additional details, see the SAMSON side-chain NSL reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.