When working with complex molecular systems, understanding and managing the size of your models is often essential. Whether you’re running simulations, visualizing, or preparing a publication, knowing the number of atoms—before diving deeper—can help you make decisions more efficiently and avoid unnecessary computation.
In SAMSON, the Node Specification Language (NSL) makes it easy to select and filter molecular structures based on specific criteria. One of the most practical filters is by number of atoms, using the numberOfAtoms attribute in the structuralModel attribute space.
Why filter by number of atoms?
- Performance optimization: Avoid loading huge models that might strain your resources.
- Simulation targeting: Select only structures suitable for certain computational methods.
- Dataset segmentation: Organize your models based on complexity and size.
Getting started with sm.nat
In NSL, atom count filtering is done using the numberOfAtoms attribute, or sm.nat for short. This attribute matches structural models with a given number of atoms and supports exact values, ranges, and inequalities.
Examples:
sm.nat > 100— Selects all molecular models with more than 100 atoms.sm.nat 100:200— Targets models with 100 to 200 atoms.sm.nat < 500— Useful for filtering out massive structures and focusing on smaller molecules.
Combining with other attributes
One of the strengths of NSL is combinatorial filtering. For example, you could combine atom count with visibility and selection flags:
sm.nat > 150 and sm.v— Structures with more than 150 atoms that are currently visible.sm.nat 200:500 and not sm.h— Models with 200–500 atoms that are not hidden.
When to use atom count filters
Here are some practical situations where filtering by sm.nat can save time and streamline your workflow:
- Dataset exploration: If you’ve imported hundreds of models, identify intermediate-sized models quickly.
- Preparing for quantum calculations: Limit selections to models below a certain size to avoid computational bottlenecks.
- Creating visualizations: Focus on manageable models for cleaner illustrations.
As with other NSL filters, sm.nat integrates directly into SAMSON’s selection interface. Simply type your expression into the NSL field and SAMSON will highlight matching models instantly. It’s a small trick that can make a big difference in managing molecular complexity.
To learn more about numberOfAtoms and other helpful filtering attributes in SAMSON, visit the Structural Model Attributes section of the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.