Exploring Backbone Attributes in Molecular Models

When molecular modelers delve into structural analysis, understanding which nodes or structural groups share key attributes becomes invaluable. One such crucial feature in SAMSON’s Node Specification Language (NSL) is the detailed mapping of backbone attributes. This post will walk you through their significance and practical applications, especially when working with the backbone nodes in your molecular models.

Why Backbone Attributes Matter

Backbone attributes are primarily defined in the backbone attribute space (short name: s) and only match backbone nodes. These attributes provide parameters that allow granular control over your molecular system, letting you filter, modify, or highlight specific nodes based on a range of criteria like visibility, material properties, or chemical composition.

Key Backbone Attributes Overview

Below are some attributes that can transform how you query and manipulate your molecular data:

  • visible (v): Determines whether a node is visually displayed. Queries such as bb.v or not bb.v can be pivotal during visualization.
  • hasMaterial (hm): Identifies if the backbone possesses any material. Use bb.hm or not bb.hm when filtering materialized vs. non-materialized nodes.
  • name (n): Allows string-based querying of node names within quotes. Examples include bb.n "Water" or bb.n "C*" for wildcard queries.
  • formalCharge (fc): Useful for charged species, this attribute narrows down structural groups with specific integer charges. For instance, you might use bb.fc > 1 or bb.fc 3:5 to find nodes with specific charge ranges.
  • numberOfAtoms (nat): Queries the total number of atoms in a node. Create queries like bb.nat < 100 or bb.nat 50:150 to analyze groups of interest.

These attributes—and many more in the documentation—enable enhanced workflows tailored to molecular design. Queries can be combined to home in on multiple characteristics with remarkable precision.

Practical Example

Imagine working with a molecular model where you need to visualize backbone nodes containing more than 10 carbons while filtering out those lacking associated materials. By combining attributes like numberOfCarbons and hasMaterial, you can structure a query such as:

This single-line query saves significant time, providing focused analysis and clear visualization.

Inherited Backbone Attributes

Some backbone attributes are inherited from NSL’s node and structuralGroup spaces, establishing a unified attribute language. For example:

  • hidden (h): From node, denoting whether a backbone node should be hidden from view.
  • partialCharge (pc): From structuralGroup, informational when mapping charge distributions across molecules (bb.pc 1.5:2.0).

Final Thoughts

The backbone attribute space in SAMSON provides powerful tools for navigating and analyzing large, complex molecular structures. Whether you’re inspecting visible surfaces, focusing on charged groups, or querying based on material ownership, this functionality helps streamline operations and enhances precision in molecular modeling tasks.

For a complete breakdown of all backbone attributes and their definitions, visit the detailed SAMSON documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at www.samson-connect.net.

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