Simplify Molecular Modeling with Conformation Attributes in SAMSON

Molecular modelers often spend significant time navigating complex datasets to identify specific conformations for their structures. Filtering through extensive molecular data to locate, for instance, conformations with a certain number of atoms or specific selection criteria can be daunting without appropriate tools. Luckily, SAMSON’s Node Specification Language (NSL) offers a solution by providing access to conformation attributes, enabling users to streamline modeling workflows.

This blog post delves into how the conformation attribute space in SAMSON can help you easily explore and filter conformations based on specific attributes. Whether you’re new to SAMSON or a seasoned user, understanding conformation attributes can significantly enhance your efficiency.

What Are Conformation Attributes?

Conformation attributes belong to the conformation attribute space, which matches only conformation nodes. These attributes allow modelers to define flexible queries for their structures, such as finding nodes based on attributes like the number of atoms (numberOfAtoms) or selection status (selected).

How to Use Conformation Attributes

The conformation attribute space has both inherited and specific attributes for conformations:

Inherited Attributes

name (short name: n): This lets you filter conformations based on their names. For example, co.n "A" matches conformations named “A”. Adding wildcards such as co.n "L*" broadens the scope to names starting with “L”.
selected: Matches conformations that are selected (true) or not selected (false). For example, you could use co.selected to find all selected conformations or use not co.selected to exclude them.
selectionFlag (short name: sf): Filters based on a custom selection flag (true or false). Examples include co.sf and co.sf false.

Specific Attributes

The most useful attribute specific to conformations is numberOfAtoms (short name: nat), which matches conformations based on the number of atoms:

For conformations with more than 100 atoms, use co.nat > 100.
To limit your search to conformations with atoms ranging between 100 to 200, use co.nat 100:200.

These precise specifications make it easier to locate the exact conformation(s) you need in your project, cutting down significant manual searching time.

Example Use Case

Suppose you’re modeling a protein-ligand interaction and need to review conformations with more than 150 atoms and haven’t been specifically selected yet. Using the conformation attribute space in the NSL, you could write:

co.nat &gt; 150 and not co.selected

1	co.nat > 150 and not co.selected

This simple but powerful query locates the exact nodes of interest, ensuring your focus stays on relevant data.

Wrapping Up

The conformation attribute space in SAMSON’s NSL provides a robust way for molecular modelers to query and analyze conformations efficiently. With these tools at your disposal, you can filter specific conformations using attributes like numberOfAtoms, selected, or name, making it easier to focus on the models that truly matter to your research.

To explore more about conformation attributes and their applications, visit the complete documentation page here: Conformation Attributes Documentation.

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