When a molecular project contains several conformations, finding the ones with the right size can be a practical first step. A name may not tell you how large a conformation is, and scanning a long list one entry at a time can become tedious. In SAMSON, the conformation attribute numberOfAtoms lets you filter conformations by atom count using the Node Specification Language (NSL).
Start with the atom-count attribute
The full attribute is conformation.numberOfAtoms; its short form is co.nat. It matches conformation nodes according to their number of atoms, and its values are integers. For example:
|
1 |
co.nat > 100 |
This selects conformations with more than 100 atoms. The equivalent longer expression is:
|
1 |
conformation.nat > 100 |
The short form is convenient for repeated use, while the full form can make a query easier to read when you are learning the attribute or sharing an expression with someone unfamiliar with its abbreviation.
Use a range when size is the constraint
If you are looking for conformations within a particular size band, use a range:
|
1 |
co.nat 100:200 |
This matches conformations with a number of atoms between 100 and 200. The same query can be written as conformation.nat 100:200. A range is useful when a single cutoff would return too many results, or when you already know the approximate size you want to inspect.
Make the query answer one clear question
Before writing an expression, translate the problem into a simple condition: “more than 100 atoms” becomes co.nat > 100; “between 100 and 200 atoms” becomes co.nat 100:200. That small step helps prevent a common source of confusion: using an attribute name that describes a different property. Here, nat is the short name for atom count, not a name or selection attribute.
For example, if a set of conformations feels too large to review, a count-based query can reduce it to those above a chosen threshold. If you want to focus on a narrower size group, use a range instead. These expressions do not describe why a conformation has that atom count; they simply provide a criterion for matching conformations. Treat the result as a size-based filter, then use the rest of your modeling context to decide which conformations are relevant.
Keep inherited attributes separate from atom count
The conformation attribute space also inherits node attributes such as name, selected, and selectionFlag. Those describe different properties. For instance, co.n "A" refers to a name, whereas co.nat > 100 refers to atom count. The similar-looking short forms make it especially useful to check the attribute name when a query does not express the condition you intended.
In short: use co.nat when the question is about how many atoms a conformation contains, choose a threshold or range that reflects your search, and keep name or selection criteria conceptually distinct. For the complete attribute reference and additional examples, see the SAMSON conformation attributes documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.