A molecular scene can contain models of very different sizes and compositions. When you need to find a large structure, check whether a model contains a particular number of chains, or locate models with an unusual charge, scanning names and structures one by one can become tedious. Structural-model attributes in SAMSON’s Node Specification Language (NSL) let you describe these properties as searchable criteria.
The useful distinction is that these attributes describe a structural model as a whole. For example, sm.nat refers to the model’s number of atoms, while sm.nr refers to its number of residues. This makes them a good starting point for model-level triage: first narrow down which structures deserve attention, then inspect their details.
Start with size
If you are looking for a sizeable structure, try sm.nat > 100. To focus on models with an atom count between 100 and 200, use sm.nat 100:200. These are examples of the integer comparisons and ranges supported by the attribute.
Atom count is not the only useful measure of size. A model’s residue count can help when working with protein structures: sm.nr > 100 matches models with more than 100 residues, and sm.nr 100:120 specifies a range. The number of chains and molecules can help answer different questions: sm.nc < 3 looks for fewer than three chains, while sm.nm 2:4 looks for models with two to four molecules.
Use composition to narrow the search
When two models have similar overall size, their elemental composition can be a more informative clue. NSL includes counts for carbon, hydrogen, nitrogen, oxygen, and sulfur. For example, sm.nO < 10 checks for fewer than ten oxygen atoms, and sm.nH 10:20 specifies a range for hydrogen atoms. The corresponding short names are sm.nC, sm.nH, sm.nN, sm.nO, and sm.nS.
These counts are useful for narrowing a set of candidates, not for identifying a molecule by themselves. Treat them as descriptive clues: a count can tell you that a model fits a criterion, but additional inspection may be needed to determine whether it is the structure you intended.
Check charge and organization
For charge-based searches, sm.fc represents total formal charge, while sm.pc represents total partial charge. For example, sm.fc 6:8 selects models with formal charge between 6 and 8; sm.pc 1.5:2.0 specifies a partial-charge range. Formal charge takes integer values, whereas partial charge uses real values.
Other organization counts can help describe a model before closer inspection. Use sm.ns for the number of segments, sm.nsg for the number of structural groups, and sm.ncga for the number of coarse-grained atoms. For instance, sm.ns < 3 checks for fewer than three segments. These attributes can be especially helpful when atom count alone does not distinguish the models you are comparing.
Keep the query readable
The short prefix sm identifies the structural-model attribute space, and the short attribute names make individual expressions compact. You can also write the longer attribute names, such as structuralModel.numberOfAtoms. If you are sharing a search with a colleague, the longer form may be easier to interpret at a glance; the short form is convenient for frequent use.
Structural models also inherit general node attributes, including sm.hidden, sm.visible, sm.selected, and sm.name. These describe visibility, selection, and naming rather than molecular composition. One small detail: the selected attribute has no short name in this attribute space, so use sm.selected.
A practical approach is to begin with the property that best matches your question—size, composition, organization, or charge—and use the corresponding expression to narrow the candidates. Then inspect the resulting models in the context of your work. For the full attribute reference and additional examples, see the structural model attributes documentation.
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