If you’ve ever worked with large molecular systems, you know how quickly the number of conformations in a project can become overwhelming. Whether you’re analyzing protein dynamics, running conformational ensembles, or simply loading a PDB with alternate locations, data clutter from numerous conformations can hinder productivity and slow down analysis.
One particularly handy solution in SAMSON’s Node Specification Language (NSL) is its ability to filter conformations based on the number of atoms. This makes it easy to zoom in on model elements that meet specific atom-count criteria—ideal for identifying fragments, larger molecular assemblies, or even busting outliers in a dataset.
What makes this useful?
Let’s say you simulate a drug-binding pocket across 500 conformations, but some of them lost atoms in the process (maybe due to errors in preprocessing). Instead of locating faulty conformations manually, you can apply a simple NSL filter and highlight only the conformations with, say, fewer than 120 atoms. Or maybe you’re interested only in protein fragments within a certain atom-count range. NSL makes this efficient and replicable.
The numberOfAtoms Filter
Within SAMSON’s NSL, conformations have access to a namespace called conformation (short form: co), which includes an attribute named numberOfAtoms (short name: nat).
This attribute lets you select conformations with a defined number of atoms. Here’s how to use it:
co.nat > 100— matches conformations that contain more than 100 atomsco.nat 100:200— matches conformations with atom counts between 100 and 200
Application Examples
Here are a few realistic use cases that make filtering by atom count useful:
1. Quality Control in Model Import
If you’ve just imported a complex structure and want to make sure all conformations are fully loaded, a filter like co.nat > 200 can help exclude damaged or partial conformations from further analysis.
2. Focusing on Small Molecules
Suppose you’re only interested in ligand conformations within a simulation. A quick filter like co.nat < 50 will trim the data to just the small molecules.
3. Selecting a Range for Ensemble Profiling
Want to batch-process conformations only if they lie within a specific size range? co.nat 150:250 selects exactly that subset.
How to Use It
You can enter these expressions directly into tools that accept NSL queries in SAMSON, like selection filters or scripting modules. The flexibility also makes this useful in automating workflows that might require atom-count-based logic.
Quick Reference
Here’s the syntax at a glance:
| Expression | Description |
|---|---|
co.nat > 100 |
Conformations with more than 100 atoms |
co.nat 100:200 |
Conformations with 100–200 atoms |
co.nat <= 80 |
Conformations with 80 atoms or fewer |
Where to Learn More
To explore additional conformation attributes and filtering capabilities, check out the full documentation page for conformation attribute space in SAMSON’s NSL: https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.