A Faster First Pass: Find the Structural Models That Need Attention

When a scene contains several molecular structures, it can be hard to know where to investigate first. A model may be unexpectedly large, contain more chains or residues than expected, or have a charge that warrants a closer look. Checking each structure manually can turn a quick review into a tedious one.

SAMSON’s Node Specification Language (NSL) offers a practical first-pass approach: filter structural models by properties such as atom count, chain count, residue count, and charge. These filters do not explain why a model has a particular property, but they can help you narrow the set of models to inspect.

Start with the scale of the model

For a quick size check, use sm.nat, the short name for numberOfAtoms. For example:

  • sm.nat > 100 finds structural models with more than 100 atoms.
  • sm.nat 100:200 finds models with an atom count in the 100–200 range.
  • sm.nat < 1000 finds models with fewer than 1,000 atoms.

A range can be useful when you already have an expected size in mind; a comparison can help flag models above or below a rough cutoff. Treat these as screening criteria, not as judgments about whether a model is correct. The relevant cutoff depends on what you are working with.

Use structural counts to spot unexpected complexity

Atom count is only one kind of complexity. If the question is about organization, try the model-level counts instead:

  • sm.nc < 3 checks for models with fewer than three chains.
  • sm.nc 2:4 checks for models with two to four chains.
  • sm.nm < 3 checks for models with fewer than three molecules.
  • sm.nr > 100 checks for models with more than 100 residues.
  • sm.ns > 2 checks for models with more than two segments.

These attributes answer different questions. A model’s number of chains is not the same as its number of molecules, and neither is a substitute for residue count. Choosing the count that matches your concern helps make a filter meaningful. For example, if you are checking whether a structure contains an unexpectedly long polymer, residue count may be more informative than molecule count.

Check composition and charge

NSL also provides counts for selected elements. The short names include sm.nC for carbon, sm.nH for hydrogen, sm.nN for nitrogen, sm.nO for oxygen, and sm.nS for sulfur. For instance, sm.nO 10:20 filters for models with 10–20 oxygen atoms. Such counts can help identify structures whose composition deserves a closer look; they do not identify which particular atoms are responsible.

For charge checks, use sm.fc for formal charge and sm.pc for partial charge. Examples include sm.fc 6:8 for formal charge in the 6–8 range and sm.pc 1.5:2.0 for partial charge in the 1.5–2.0 range. Formal charge uses integer values, while partial charge uses real values.

Keep the scope clear

The prefix sm refers to the structural-model attribute space, which matches structural model nodes. That distinction matters: these filters are for comparing models, rather than selecting individual atoms by their own attributes. NSL also exposes inherited node properties, including visibility and selection. For example, sm.v matches visible structural models, and not sm.selected matches unselected ones.

A useful routine is to begin with one question—size, organization, composition, charge, or visibility—then choose the corresponding attribute and a sensible comparison or range. Review the resulting matches in context before deciding what they mean. This makes NSL a way to focus inspection, not a replacement for scientific judgment.

For the full 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.

Comments are closed.