When a molecular project contains many conformations, it can be difficult to quickly narrow the list to structures of a useful size. You might be looking for larger candidates to inspect, or want to focus on a particular atom-count range. Searching by name alone may not help—especially when names are generic or inconsistent.
SAMSON’s Node Specification Language (NSL) provides a direct way to filter conformation nodes by their number of atoms. The key attribute is numberOfAtoms, abbreviated nat, in the conformation attribute space, abbreviated co. That gives you a compact query such as:
co.nat > 100
This matches conformations with more than 100 atoms. It is useful when you want to narrow a set by scale without relying on labels. You can also write the attribute in its longer form:
conformation.numberOfAtoms > 100
The short form is convenient for repeated use; the long form can be easier to recognize when you are learning the query language or sharing a query with someone unfamiliar with its abbreviations.
Use a range when size matters
A threshold is helpful when you need to exclude small conformations, but sometimes you have a target interval in mind. NSL supports a colon-separated range:
co.nat 100:200
This matches conformations with an atom count between 100 and 200. For example, a range can help you focus your review on structures of a comparable size rather than mixing much smaller and larger conformations in the same search. The documentation also gives the longer equivalent, conformation.nat 100:200.
One small but useful habit: keep the attribute and its value together as shown. The count is queried with nat; a name query uses n. For instance, co.n "A" searches by name, while co.nat > 100 searches by atom count. Choosing the attribute that matches the question makes a query easier to read and reduces the chance of filtering on the wrong property.
Make sure you are querying conformations
The co prefix matters. It identifies the conformation attribute space, which matches conformation nodes. This is different from writing a broad query without specifying the node type: if your goal is to find conformations by their atom count, use the conformation space explicitly. That makes the intent of the query clear, particularly when you revisit it later or pass it to a collaborator.
Conformation nodes also inherit several general node attributes. For example, co.n "A" searches by name, co.selected tests whether a conformation is selected, and co.sf false checks its selection flag. These can be useful alongside atom-count filtering when you need to distinguish conformations by more than size. The selection attribute has no short name in this space, so use selected rather than assuming a one-letter abbreviation.
A practical query checklist
- Need conformations above a cutoff? Try
co.nat > 100. - Need conformations within a size interval? Try
co.nat 100:200. - Need to search by label instead? Use the name attribute, such as
co.n "A". - Want the query to be self-explanatory? Use the full form
conformation.numberOfAtoms.
These queries turn atom count into a practical first-pass filter: instead of inspecting every conformation individually, you can define the size criteria you care about and focus your attention on the resulting matches. For the complete attribute reference and additional examples, see the SAMSON conformation attributes documentation.
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