Large molecular projects can contain many structural models, and finding the one you need by browsing them individually can be tedious. Maybe you are looking for a model of a certain size, a system with several chains, or a structure whose charge falls within a particular range. SAMSON’s Node Specification Language (NSL) lets you describe these criteria using structural-model attributes.
The useful idea is to turn a vague browsing task into a small set of specific questions. Structural-model attributes match structural model nodes, so they are suited to screening models by properties such as atom count, chain count, residue count, and charge. The attribute space uses the prefix structuralModel, or the shorter prefix sm.
Start with the size of the model
If you want to narrow a collection by overall size, use numberOfAtoms, abbreviated nat. For example, sm.nat < 1000 matches structural models with fewer than 1,000 atoms. To look within a band, use a range: sm.nat 100:200 matches models with between 100 and 200 atoms.
This is a practical first pass when you know roughly how large the target system should be. It can help separate small molecules or compact systems from much larger structures before you inspect details. The same style of numeric comparison works for many other count attributes.
Use structural counts to describe composition
Atom count alone may not tell you whether a model has the organization you expect. To screen by chains, use sm.nc: sm.nc < 3 looks for models with fewer than three chains, while sm.nc 2:4 matches the documented range from two to four chains.
Other useful counts include residues (sm.nr), molecules (sm.nm), segments (sm.ns), and structural groups (sm.nsg). For example, sm.nr > 130 can help identify models with more than 130 residues, and sm.nm 2:4 can help find models containing between two and four molecules.
There are also element-specific counts: sm.nC for carbon, sm.nH for hydrogen, sm.nN for nitrogen, sm.nO for oxygen, and sm.nS for sulfur. For example, sm.nO < 10 matches models with fewer than ten oxygen atoms. These attributes provide a quick way to check whether a model’s elemental composition is broadly consistent with what you expect.
Keep formal and partial charge distinct
Charge is another useful screening criterion, but the documentation distinguishes two kinds. sm.fc refers to total formal charge and accepts integers. For instance, sm.fc 6:8 matches models with formal charge between six and eight.
sm.pc refers to total partial charge and accepts real numbers. The expression sm.pc 1.5:2.0 matches models with partial charge between 1.5 and 2.0. Keeping these attributes separate matters: they represent different documented properties, so choose the one that corresponds to the question you are trying to answer.
A simple screening routine
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Write down the properties you know: approximate size, expected chain or residue count, and any relevant charge information.
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Use one attribute at a time to check each criterion. For example, start with
sm.nat 100:200, then examine chain count withsm.nc 2:4. -
Use the full attribute names when they are easier to read, such as
structuralModel.numberOfResidues > 100; use short forms such assm.nr > 100for compact expressions. -
Inspect the matches in the context of your project. Numeric filters can narrow the search, but the counts alone do not establish whether a model is scientifically appropriate.
NSL also lists inherited attributes for structural models, including sm.visible, sm.hidden, and sm.selected. These can help describe visibility or selection state, while the count and charge attributes focus on model properties. Together, they give you a vocabulary for making model searches more deliberate instead of relying only on manual browsing.
For the complete attribute reference and additional examples, see the SAMSON structural model attributes documentation.
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