Molecular modelers often face the challenge of filtering and working with highly specific data within complex molecular systems. In SAMSON, you can easily manage molecular chains and their properties using the chain attribute space, which can drastically simplify your modeling workflow.
The chain attribute space (short name: c) in SAMSON’s Node Specification Language (NSL) is tailored to query and manipulate chain nodes efficiently. By leveraging these attributes, you can quickly access, filter, or manipulate chains according to specific criteria. Let’s explore some of the powerful chain attributes you can utilize for precision filtering or analysis.
Streamline Your Workflow with Key Chain Attributes
The chain attribute space offers a range of attributes—some inherited from other attribute spaces and some specific to chain nodes. These attributes allow you to precisely describe chains in your molecular models. Below, we highlight some key attributes:
Attributes for General Interaction
| Attribute Name | Short Name | What It Does |
|---|---|---|
| name | n |
Filters chains based on their names. Useful for identifying and working with specific chains. |
| hasMaterial | hm |
Matches chains that either possess or do not possess material (true / false). |
| visible | v |
Determines chain visibility within the molecular model (true / false). |
Analyze Structural and Quantitative Data
If your molecular research involves analyzing structural complexity, SAMSON offers attributes that expose detailed chain-level information:
| Attribute Name | Short Name | What It Measures |
|---|---|---|
| numberOfResidues | nr |
Counts the number of residues in a chain (c.nr). |
| numberOfAtoms | nat |
Tracks the total number of atoms in a chain (c.nat). |
| numberOfNitrogens | nN |
Focuses on counting nitrogen atoms specifically. |
Flexible Querying with Examples
SAMSON’s Node Specification Language makes querying easy with concise syntax. For example:
c.n "A": Matches chains with the nameA.c.nr > 100: Filters chains with more than 100 residues.c.visible: Identifies visible chains.
These queries ensure your focus is automatically narrowed to the most relevant chains.
Conclusion
Mastering these chain attributes in SAMSON will give you unparalleled control over your molecular modeling process. Whether you are aligning chains, analyzing structural data, or creating visual representations, these tools can significantly reduce the time and effort required for complex tasks.
For a full list and detailed descriptions of chain attributes, visit the official documentation page here: Chain Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.