When a molecular structure contains thousands of atoms, a simple question—“Which atoms could participate in hydrogen bonding?”—can quickly become a selection problem. Hydrogens may clutter the view, protein backbones and side chains may need separate attention, and an atom’s element alone does not tell you whether it is classified as a donor or acceptor.
SAMSON’s Node Specification Language (NSL) lets you build focused selections from atom attributes. The useful starting point is to treat donor, acceptor, and hydrogen as distinct searches, then combine them only when a task calls for it.
Start with donors and acceptors
Use the hydrogen-bond attributes to select atoms classified as donors or acceptors:
a.hbdselects hydrogen-bond donors.a.hbaselects hydrogen-bond acceptors.a.hbd or a.hbaselects atoms matching either attribute.
This is more informative than selecting every nitrogen or oxygen. Element-based searches such as a.s N or a.s O are useful when you want all atoms of an element, but donor and acceptor attributes let you ask a more chemically specific question.
One important distinction: these selections identify atoms with donor or acceptor attributes; they do not, by themselves, establish that a particular hydrogen bond is formed between two atoms. Treat them as a way to narrow the structure for inspection, not as proof of an interaction.
Keep hydrogen atoms in context
When you need to inspect hydrogen atoms, use a.hp to select polar hydrogens. The documentation defines polar hydrogens as hydrogen atoms attached to atoms with significantly larger electronegativity: N, O, S, F, or Cl. This can help distinguish them from the larger set of atoms in a structure.
For donor-linked hydrogens, use a.dbh. This attribute matches donor-borne hydrogens in hydrogen bonds. It answers a different question from a.hbd: one selects donor atoms, while the other selects the associated donor-linked hydrogens.
To focus on non-hydrogen atoms, use a.nonH, the short name for the heavy attribute. For example, a.hba and a.nonH expresses a selection of heavy atoms that are acceptors. Being explicit can make a query easier to read and adapt, especially when you are moving between atom-level and hydrogen-level selections.
Limit the search to a structural region
For a protein-focused selection, NSL also provides a.aabb for heavy atoms belonging to an amino-acid backbone. You can combine it with an acceptor or donor condition, for example:
a.hba and a.aabb— backbone heavy atoms classified as acceptors.a.hbd and a.aabb— backbone heavy atoms classified as donors.
These combinations are useful when you want to inspect backbone contributions without first selecting every atom in the structure. If you are investigating a different region, use the relevant structural attributes available in NSL and combine them with the same donor or acceptor criteria.
A simple selection workflow
- Begin with
a.hbdora.hba, depending on whether you are examining donors or acceptors. - Add
a.nonHif you want to keep the selection focused on heavy atoms. - Use
a.hpora.dbhwhen the hydrogen atoms themselves are relevant. - Add a structural filter such as
a.aabbto narrow the selection to backbone atoms. - Inspect the selected atoms in the molecular context before drawing conclusions about actual interactions.
The benefit of this approach is not just a smaller selection. It keeps different chemical questions separate: which atoms are donors, which are acceptors, which hydrogens are polar, and which atoms belong to the backbone. That makes it easier to refine a search without relying on element identity alone.
For the complete list of atom attributes, aliases, values, and examples, see the SAMSON atom attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.