The world of molecular modeling is intricate, often requiring precise customizations to understand and manipulate molecular structures effectively. That’s where the Node Specification Language (NSL) in SAMSON becomes indispensable, offering users a structured way to define and refine molecule attributes. In this post, we’ll walk you through attributes specific to the molecule attribute space in NSL, and how leveraging them can address common challenges in molecular modeling.
Why Molecule Attributes Matter to Modelers
In a busy workflow, isolating molecules based on their structural properties—for instance, the number of chains or residues—can help speed up calculations, ensure better visualization, and refine simulations. Questions like “How can I easily filter molecules with more than 100 residues?” or “Can I detect molecules with fewer than three structural groups?” are common pain points. With NSL, these operations can be automated and simplified, making your molecular modeling process faster and more efficient.
Diving Into Molecule-Specific Attributes
SAMSON’s NSL provides an extensive set of molecule-specific attributes, with short names for quick usage. These attributes allow you to set criteria, filter, and control molecules based on their intrinsic properties.
| Attribute Name | Short Name | Possible Values | Examples |
|---|---|---|---|
numberOfChains |
nc |
integers |
mol.nc < 3mol.nc 2:4
|
numberOfResidues |
nr |
integers |
mol.nr > 130mol.nr 100:130
|
numberOfSegments |
ns |
integers |
mol.ns > 2mol.ns 2:4
|
numberOfStructuralGroups |
nsg |
integers |
mol.nsg > 10mol.nsg 10:12
|
Common Use Cases for Exceptional Modeling
Here are some scenarios where molecule-specific attributes make a difference:
- Filtering molecules by structural complexity: Use
mol.nc < 3to identify molecules with fewer than three chains. This is particularly helpful when isolating smaller or simpler molecules for analysis. - Investigating large assemblies: If you are studying macromolecular complexes,
mol.nr > 100helps you filter larger molecules based on the number of residues. - Refining selections based on chemical hierarchies: For molecules divided into segments, try
mol.ns 2:4to narrow down structures with segments only within this range. - Optimizing workflows: Use selections like
mol.nsg > 10to exclude simpler molecules with fewer structural groups, which might not be relevant for your investigation.
Speeding Up Commands with Short Names
Short names (e.g., nc, nr) allow writing efficient and compact queries. For instance, instead of typing molecule.numberOfChains 2:4, mol.nc 2:4 achieves the same result with less effort, saving precious time for iterative modeling tasks.
Expand Your Expertise
Understanding and leveraging NSL attributes is crucial for working efficiently in SAMSON. By mastering molecule-specific attributes, you’ll gain better control over the structure and selection processes, significantly reducing the complexity of your projects.
For more details and a deeper dive into all available attributes, visit the NSL Molecule Attributes documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.