When a molecular project contains many conformations, it can be hard to find the ones that are relevant to a particular task. A useful first step is to narrow the search by size: for example, find conformations with more than 100 atoms, or focus on those whose atom counts fall between 100 and 200. In SAMSON, the Node Specification Language (NSL) lets you express these searches with the conformation attribute space.
Start with the conformation attribute space
The full attribute-space name is conformation, and its short name is co. This space matches conformation nodes, so it gives your query a clear scope. For example, these two expressions are equivalent:
conformation.nat > 100co.nat > 100
Here, nat is the short name for numberOfAtoms. The expression asks for conformations with more than 100 atoms. Using the short form makes repeated searches quicker to type; the full form can be easier to read when you are learning the attribute names or sharing a query with someone else.
Choose a threshold or a range
A threshold is handy when you want to separate smaller conformations from larger ones. For instance, co.nat > 100 can help you focus on conformations above that size. Change the number to suit the scale of the structures in your project.
If you already have a useful interval in mind, use a range:
co.nat 100:200
This matches conformations with a number of atoms between 100 and 200. A range can be a practical way to avoid looking through every conformation individually when you are interested in a particular size band. The documentation describes this as “between 100 and 200”; if the exact treatment of the endpoints matters for your task, verify it in your SAMSON workflow rather than assuming whether the bounds are inclusive.
Keep the query focused
NSL also provides attributes inherited from the general node attribute space. For conformations, these include name, selected, and selectionFlag. The name can be searched with quoted text, for example co.n "A". The selection state can be tested with co.selected or not co.selected, while co.sf is the short name for selectionFlag.
These attributes address different questions: atom count describes conformation size, name describes its label, and selection-related attributes describe its selection state. Keeping those distinctions in mind makes it easier to choose the right attribute when a search returns more—or fewer—results than expected. The conformation page notes an important detail: selected is inherited without the short name s in this attribute space. Use co.selected rather than assuming the node-space shorthand applies here.
A simple way to use the filter
- Decide whether you need a cutoff or a bounded interval.
- Write the query using
co.nat, such asco.nat > 100orco.nat 100:200. - Check whether the result set is the right size for your next inspection step, then adjust the number or interval if needed.
The benefit is straightforward: instead of treating every conformation as equally relevant, you can use a concrete, measurable property to narrow your search. That can make browsing a large set less tedious and help you return to a reproducible query later.
For the complete attribute list and syntax examples, see the SAMSON conformation attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.