When a molecular scene contains several structures, it can be surprisingly hard to find the one you need. A name may be unclear or unhelpful; a quick visual scan may not tell you whether a molecule is a small ligand, a long chain, or a multi-chain assembly. In SAMSON, the Node Specification Language (NSL) offers another way to narrow the search: describe molecules by measurable attributes, then use those criteria to identify matching molecule nodes.
This is especially useful when your first question is not “What is this molecule called?” but “How large is it?”, “How many residues does it contain?”, or “Does it have more than one chain?” The molecule attribute space uses the short prefix mol and matches molecule nodes.
Choose a count that answers your question
Different counts help separate different kinds of structures. mol.nat refers to the number of atoms, while mol.nr refers to the number of residues. For example, these documented expressions match molecules with fewer than 1,000 atoms or more than 100 residues:
mol.nat < 1000mol.nr > 100
Residue count can be a useful first pass when you are looking for a larger biomolecular structure among smaller molecules. Atom count gives a different measure of size. Neither count tells the whole story, so select the attribute that fits the distinction you are trying to make.
If you already have a useful interval in mind, a range can make the criterion more specific. For instance, mol.nr 100:120 matches molecules with a number of residues between 100 and 120. The documentation also gives mol.nat 100:200 as an atom-count range.
Use organization counts to find assemblies
A molecule’s organization can be more informative than its overall size. The short attribute mol.nc represents the number of chains. The expression mol.nc < 3 matches molecules with fewer than three chains; mol.nc 2:4 matches molecules with a chain count between two and four.
Other organization counts can help describe what you are looking for. mol.ns is the number of segments, and mol.nsg is the number of structural groups. For example, mol.ns > 2 matches molecules with more than two segments, while mol.nsg > 10 matches those with more than ten structural groups. These attributes give you ways to express structural organization without relying only on a molecule’s name.
Check composition or charge when size is not enough
For another angle, inherited structural-group attributes include counts of particular elements. Examples include mol.nC < 10 for fewer than ten carbons and mol.nO 10:20 for an oxygen count between ten and twenty. Molecules can also be matched by formal charge: mol.fc > 1 is one documented example. These criteria can help distinguish candidates that have similar overall sizes but different compositions or charge properties.
A practical way to narrow the search
- Start with the distinction you care about. Choose atom count, residue count, chain count, or another relevant attribute.
- Use a broad condition first. For example, try
mol.nr > 100if you are looking for molecules with many residues. - Refine with a second characteristic. Check chain count, element counts, or formal charge to describe the candidates more precisely.
- Use ranges when you know the scale. Expressions such as
mol.nc 2:4make a bounded criterion easy to read.
The examples above are individual NSL expressions; they illustrate the available molecule attributes rather than prescribing a particular way to combine filters. A helpful habit is to write down what you know about the target first—size, organization, composition, or charge—then choose the matching attribute. Short names keep expressions compact, while the full names, such as molecule.numberOfResidues, can be easier to interpret when you are learning the language.
For the complete attribute reference and more examples, see the SAMSON molecule attributes documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.