When working with complex molecular models, it’s common to end up with large systems composed of many different molecules, chains, residues, or even entire assemblies. Navigating this complexity can be time-consuming and error-prone, especially when your goal is to focus on specific types of molecules. For example, you might want to:
- Identify molecules with more than 100 residues
- Select molecules containing a specific number of chains
- Filter according to structural complexity, such as residues, segments, or structural groups
This is where the Node Specification Language (NSL) in SAMSON becomes extremely useful. In particular, the molecule attribute space helps modelers filter, select, and organize molecular data based on specific molecule-level characteristics.
Why Filter by Molecular Attributes?
Let’s say you’re preparing a molecular model for simulation or analysis. Selecting molecules that meet certain criteria—such as size, visibility, or formal charge—helps streamline your workflow and ensures higher-quality results. For instance, you might want to exclude water molecules, select molecules above a certain size, or isolate only molecules involved in a specific chain.
Below are key attributes available in the mol attribute space and practical examples of how to use them.
Number of Chains (mol.nc)
Filters molecules based on how many chains they contain.
mol.nc < 3: matches molecules with fewer than three chainsmol.nc 2:4: selects molecules with 2 to 4 chains
Number of Residues (mol.nr)
Focuses on structural complexity by considering how many residues are present.
mol.nr > 130: finds larger biomolecules with more than 130 residuesmol.nr 100:130: provides a range for mid-sized proteins
Number of Segments and Structural Groups
mol.ns > 2: useful for molecules with multiple functional regionsmol.nsg > 10: pinpoints complex molecules with many sub-units or groups
Putting It All Together
NSL lets you combine these filters to perform advanced queries. For example, the following filter will highlight large, multi-chain, and structurally rich molecules:
|
1 |
mol.nc > 2 and mol.nr > 100 and mol.nsg > 10 |
This expression allows you to quickly isolate relevant parts of your model while hiding less pertinent ones, saving time and computational resources. You can apply such filters directly in the search bar when using NSL-compatible features, and these are especially handy before simulations, exporting structures, or assigning materials.
Whether you’re working in macromolecular modeling, molecular dynamics, or drug design, mastering molecule-level filtering is a significant boost to your precision and efficiency.
To explore the full list of NSL molecule attributes, including more examples, visit the SAMSON documentation:
https://documentation.samson-connect.net/users/latest/nsl/molecule/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.