Streamline Molecular Modeling with Molecule Attributes in SAMSON

For molecular modelers and computational chemists, managing the diverse properties of molecules efficiently can make a tremendous difference in productivity. SAMSON provides a sophisticated solution to this challenge through its molecule attributes. These attributes not only simplify filtering and querying molecular data but also help maintain a cleaner and more organized workflow. Below, we’ll explore some key molecule attributes that can be incredibly useful, how they work, and why they matter in your everyday modeling tasks.

What Are Molecule Attributes?

In SAMSON, molecule attributes allow you to target and manipulate specific molecule nodes by accessing their associated properties. These attributes are defined within the molecule attribute space (short name: mol), enabling users to filter molecules based on characteristics like visibility, number of chains, or material ownership. The attribute syntax also supports concise shortcuts for quick commands, saving time in scripting and execution.

Key Attributes to Empower Your Work

Let’s dive into some significant molecule attributes you can leverage:

1. Visibility and Material-Related Attributes

  • hasMaterial (mol.hm): Matches molecules based on whether a material is assigned. Use it to isolate molecules for rendering or analysis.
  • visible (mol.v): Checks if a molecule is visible. For example, not mol.v targets hidden molecules without disrupting visible ones.
  • ownsMaterial (mol.om): Identifies molecules that directly own materials.

2. Structural and Functional Attributes

  • numberOfChains (mol.nc): Determines the number of chains in a molecule. Example: mol.nc < 3 finds molecules with fewer than three chains.
  • numberOfAtoms (mol.nat): Filters molecules based on their atom count. Example: mol.nat 100:200 matches molecules with 100–200 atoms.
  • numberOfHydrogens (mol.nH), numberOfCarbons (mol.nC), etc.: These attributes provide specificity by counting particular atoms, ideal for customized queries in large systems.

Examples of Efficient Filtering

Simple queries can yield significant results while working with molecular structures in SAMSON:

  • mol.hm: Select molecules with assigned materials.
  • mol.nC 5:10: Pinpoint molecules with a number of carbons ranging from 5 to 10.
  • mol.nr > 100: Identify molecules with more than 100 residues.

These concise commands help you streamline workflows, enabling accurate selections and efficient molecular management.

Why Use Molecule Attributes?

Molecule attributes are invaluable for modelers aiming to work smarter, not harder. They eliminate the need for manual search and selection tasks that can slow down projects. Whether you’re examining visibility states for rendering, tallying specific atom types, or pinpointing residues or segments in large systems, these attributes provide clarity and precision.

Learn More

To dive deeper into the properties and commands mentioned above, visit the official documentation page for molecule attributes. Becoming proficient in using these attributes will transform the way you handle molecular models.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can access SAMSON by visiting SAMSON Connect.

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