When a project contains many structural models, finding the ones worth inspecting can become a repetitive task: open a model, check its size or composition, close it, and move on. In SAMSON, the Node Specification Language (NSL) lets you describe structural models by their attributes, so you can search by properties such as atom count, number of chains, residue count, or total charge.
This is useful for making an initial shortlist before spending time on closer visual or scientific inspection. The expressions below target structural model nodes using the sm attribute-space prefix. They are filters for organizing a search—not a substitute for checking whether a model is appropriate for your particular study.
Start with the scale of the model
If you need models in a particular size range, use numberOfAtoms, abbreviated nat. For example, sm.nat 100:200 matches structural models with between 100 and 200 atoms. To look for models above a threshold, use a comparison such as sm.nat > 100. The documentation also gives sm.nat < 1000 as an example.
For protein or other residue-based structures, sm.nr filters by number of residues. For example, sm.nr 100:130 selects models with a residue count between 100 and 130. If chain organization is more relevant, try sm.nc 2:4 for models with between two and four chains, or sm.nc < 3 for fewer than three chains. The same general pattern applies to molecules (sm.nm), segments (sm.ns), and structural groups (sm.nsg).
Use composition counts to narrow candidates
When the elements in a model matter, NSL provides counts for carbon, hydrogen, nitrogen, oxygen, and sulfur. For example, sm.nO 10:20 describes models with between 10 and 20 oxygen atoms, while sm.nS < 10 describes models with fewer than 10 sulfur atoms. Other short names include sm.nC, sm.nH, and sm.nN. There is also sm.ncga for the number of coarse-grained atoms.
These counts can help distinguish models with different compositions without relying on names alone. They are structural-model attributes: the query is about the model’s count, rather than a request to select individual atoms of a particular element.
Check charge-related properties
For total formal charge, use sm.fc. For instance, sm.fc 1 matches models with formal charge equal to 1, and sm.fc 6:8 specifies a range. For total partial charge, use sm.pc; the documented examples include sm.pc 1 and sm.pc 1.5:2.0. Formal charge takes integer values, while partial charge takes real values.
A practical way to use these attributes is to begin with the property that matters most—perhaps size, chain count, or charge—then inspect the resulting candidates and refine your search as needed. Keep the short names handy: they make expressions compact, while the full names can be easier to read when you are learning the language. The reference also lists inherited node attributes, including sm.visible, sm.hidden, and sm.selected, which can describe visibility and selection state.
For the complete attribute list and additional examples, see the structural model attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.