Mastering Structural Model Queries in SAMSON: A Guide to Attributes

Molecular modelers often face a daunting challenge when handling large and complex datasets. How do you quickly filter or analyze structural models based on specific criteria? This is where SAMSON’s Structural Model attributes step in to provide a structured approach to efficiently query molecular models and get meaningful insights.

In this post, we explore how SAMSON enables you to leverage the Structural Model attribute space, allowing you to access specific properties of structural models and streamline your modeling workflows.

What Are Structural Model Attributes?

Structural Model attributes in SAMSON are metadata associated with structural model nodes. They are part of the structuralModel attribute space (short name: sm) and allow you to manipulate or select structural models that meet specific criteria, such as the number of atoms, chains, hydrogens, or carbons.

Attributes are categorized into two types:

  • Inherited from the general node attribute space: These include attributes like visible, hidden, or selected.
  • Specific to structuralModel nodes: These include attributes like numberOfAtoms, numberOfChains, and formalCharge.

How to Use Structural Model Attributes

The structuralModel attribute space offers a set of convenient short names, enabling compact queries. For instance:

  • sm.nat > 100: Matches structural models with more than 100 atoms.
  • sm.nc 2:4: Matches structural models with 2 to 4 chains.
  • sm.nC < 10: Matches structural models with less than 10 Carbon atoms.

Examples of Common Attributes

Let’s highlight popular attributes and their use cases:

numberOfAtoms (sm.nat)

Queries based on the total number of atoms are crucial for modeling or refining large systems. You can use:

  • sm.nat 100:200: Matches models having between 100 and 200 atoms.
  • sm.nat < 1000: Matches models with fewer than 1000 atoms.

numberOfChains (sm.nc)

For multi-chain biomolecules like proteins, the chain count is often a key factor. Example:

  • sm.nc > 2: Matches models with more than 2 chains.
  • sm.nc 1:3: Focuses on small protein chains between 1 to 3.

numberOfHydrogens (sm.nH)

Hydrogens play a significant role in structural analysis, particularly in refining low-resolution models. Example:

  • sm.nH < 10: Focuses on models with under 10 hydrogen atoms.
  • sm.nH 10:20: Filters models with hydrogen atoms ranging from 10 to 20.

formalCharge (sm.fc)

Charge state impacts molecular interactions significantly. Quickly filter models with specific formal charges:

  • sm.fc 1: Matches models with a formal charge of 1.
  • sm.fc 6:8: Focuses on models whose charge lies between 6 and 8.

Why Use Queries Effectively?

Using such attributes efficiently allows you to focus on relevant nodes, saving you time and effort. Whether you’re dealing with molecular docking, drug design, or visualizing molecules, these attributes simplify your workflow by narrowing down your focus to the components of interest.

To delve deeper into all supported attributes, check out the complete documentation page at this link.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at SAMSON Connect.

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