When working with large molecular systems in SAMSON, it’s easy to get overwhelmed by the sheer number of models you’re interacting with. Whether you’re analyzing a complex simulation or preparing a presentation, you often need to isolate just the structural models that match specific criteria — perhaps models that have more than 100 atoms, or only the ones visible in the viewport.
This is where SAMSON’s Node Specification Language (NSL) can make a big difference. Using NSL attribute filters, especially for structuralModel nodes, you can select or isolate just what you need in seconds, saving time and avoiding visual clutter.
What Are Structural Model Attributes?
Structural model attributes are keywords you can use in NSL to filter or match molecular models based on their properties. These attributes belong to the structuralModel attribute space (short name: sm), and let you match nodes by characteristics like number of atoms, visibility, or even partial charge.
For example:
sm.nat > 1000→ selects structural models with more than 1000 atomssm.v→ selects visible modelsnot sm.h→ selects models that are not hidden
Common Use Cases
🔬 Selecting models with specific numbers of atoms
Whether you’re looking for orphan molecules or protein assemblies, it’s handy to filter based on atomic count:
sm.nat < 50 → quickly identifies small molecules
sm.nat 100:1000 → gets moderately sized molecular systems, common for ligands or drug candidates.
👁️ Manage model visibility
Sometimes, you’ll only want to interact with models that are currently visible or visible via a flag:
sm.v→ matches all visible modelsnot sm.v→ hides the invisible cluttersm.vf<false>→ filters by thevisibilityFlag
🧪 Identifying models by formal and partial charges
Studying charged species? Use charge filters:
sm.fc 2 → matches models with formal charge +2
sm.pc 1.5:2.0 → matches models with partial charge in a range
🧱 Filter by composition
Want to find models with many chains or specific residue complexity?
sm.nc > 2→ more than 2 chainssm.nr 100:150→ residue count rangesm.nC > 20→ carbon-rich structures
How to Use These Filters
You can use these expressions with SAMSON’s find feature, advanced selectors, or even in custom filters when scripting.
By chaining attributes and logic operators, you can create highly specific filters. For instance:
|
1 |
sm.nat > 100 and sm.v and not sm.h |
This one matches models with more than 100 atoms that are both visible and not hidden.
If you’re exploring datasets or simulations involving many structural models, mastering this filtering language can transform how you work.
To view the full list of filters and examples, visit the original documentation on structural model attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.