A molecular scene can contain many molecules, and the one you need is not always obvious from its appearance. Perhaps you are looking for a small ligand, a protein-sized structure, or a molecule with a particular number of chains. Searching by measurable properties can turn that visual hunt into a more systematic process.
In SAMSON, the Node Specification Language (NSL) lets you describe what to match. The molecule attribute space, abbreviated mol, targets molecule nodes. Its attributes include molecule-specific counts as well as properties inherited from the structural-group and node attribute spaces. That means you can search not only by the molecule’s organization, but also by atom counts, charge, name, and visibility or selection state.
Start with the kind of molecule you’re trying to find
If the distinction you care about is the number of residues, use mol.nr. For example, mol.nr > 100 matches molecules with more than 100 residues, while mol.nr 100:120 matches molecules with a residue count between 100 and 120. This can help narrow a scene to larger, residue-based structures without relying on their names.
For a chain-based search, use mol.nc. The expression mol.nc < 3 matches molecules with fewer than three chains; mol.nc 2:4 matches those with between two and four. These counts answer different questions: residues describe one level of molecular organization, while chains describe another. Choose the attribute that reflects the distinction you need to make.
Use atom counts to narrow by composition or size
The inherited mol.nat attribute matches by total number of atoms. For instance, mol.nat < 1000 can help identify molecules below a chosen size threshold, while mol.nat 100:200 selects a specific count range.
When composition matters, the same attribute space includes counts for several elements: mol.nC for carbon, mol.nH for hydrogen, mol.nN for nitrogen, mol.nO for oxygen, and mol.nS for sulfur. For example, mol.nO 10:20 matches molecules with between 10 and 20 oxygen atoms. This is a practical way to screen by a known compositional feature, though an element count alone does not identify a molecule or establish its chemical role.
For coarse-grained structures, mol.ncga counts coarse-grained atoms. Keep this separate from mol.nat: they describe different kinds of counts, so the useful measure depends on how the molecule is represented.
Don’t overlook charge and scene state
If charge is relevant, mol.fc refers to formal charge and mol.pc to partial charge. The documentation gives examples such as mol.fc > 1 and mol.pc 1.5:2.0. These attributes let you search by charge-related values rather than by structural size.
You can also search on inherited node properties. For example, mol.n "L*" searches molecule names using a quoted string, while mol.v and not mol.v distinguish visible from non-visible molecules. mol.selected checks selection state; unlike some inherited node attributes, it has no short name in the molecule attribute space.
A simple, repeatable way to search
Begin with the property you know: residue count for a residue-based structure, chain count for chain organization, total atoms for size, or an element count for composition. Try a documented threshold or range, then refine your search with another relevant property. Keeping each expression tied to a clear question makes the result easier to interpret and the search easier to repeat.
For the complete attribute list and additional examples, see the Molecule attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.