A crowded molecular workspace can make a simple question surprisingly time-consuming: which structural models are worth inspecting first? Scrolling through the scene is often a poor way to find a large model, a model with several chains, or one whose composition or charge fits your next step. SAMSON’s Node Specification Language (NSL) lets you search structural models by these properties, so you can narrow the field before opening candidates one by one.
The key is to search at the structural model level. In this attribute space, the short prefix is sm. For instance, sm.nat means the number of atoms in a structural model, while sm.nr means its number of residues. The short forms are convenient once you recognize them; the full attribute names are useful when you are learning or sharing a query.
Start with the size of the model
If you need to identify models above or below a size threshold, use numberOfAtoms. For example, sm.nat < 1000 finds structural models with fewer than 1,000 atoms. To focus on models in a range, use a colon between the limits: sm.nat 100:200. The same style applies to other integer counts, including chains, molecules, residues, and structural groups.
Different counts answer different triage questions. Use sm.nc < 3 to find models with fewer than three chains, or sm.nm 2:4 to look for models with two to four molecules. If residue count is more relevant than atom count, try sm.nr > 130. These are not interchangeable measures: a model with many atoms need not have the same residue count or chain organization as another model of similar size.
Use composition to make the search more specific
When overall size is not enough, NSL also provides element-count attributes. Examples include sm.nC for carbon atoms, sm.nH for hydrogen atoms, sm.nN for nitrogen atoms, sm.nO for oxygen atoms, and sm.nS for sulfur atoms. These accept integer comparisons and ranges, such as sm.nO 10:20. The page also lists sm.ncga for coarse-grained atoms.
This can help turn a vague inspection task into a concrete first pass: search for models with a particular atom count, then examine their element counts or chain counts to decide which ones deserve attention. You can also look at sm.nsg for the number of structural groups, or sm.ns for the number of segments.
Check charge when it matters
For charge-related screening, sm.fc filters by total formal charge, while sm.pc filters by total partial charge. Formal charge uses integer values; partial charge uses real numbers. For example, sm.fc 6:8 searches for formal charges from 6 to 8, and sm.pc 1.5:2.0 searches for partial charges in that range. These attributes describe the model’s total charge, not the charge of an individual atom.
A practical way to work
Begin with the property that most clearly separates the models you are trying to find: atom count for overall size, residue count for protein-scale organization, or chain count for assembly structure. Use a comparison such as > or < when you have a cutoff, and a range such as 100:200 when you have lower and upper bounds. Then refine your search using another relevant attribute. The documentation page gives each attribute’s full name, short name, value type, and examples, which helps avoid mixing up integer counts with floating-point partial charge.
Structural models also inherit general node attributes, including name, visible, and selected. These can help with naming or display-related searches, while the model-specific counts and charges are better suited to composition and complexity checks.
For the complete attribute reference and additional examples, see the SAMSON structural model attributes documentation.
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