Simplifying Molecular Selection: Understanding Conformation Attributes in SAMSON

For molecular modelers, filtering and analyzing molecular data efficiently is critical. Whether you are working on a protein or small molecule conformations, understanding the basics of conformation attributes in SAMSON can save time and effort. In this blog post, we will focus on these attributes and how you can use them in SAMSON’s Node Specification Language (NSL) to streamline your molecular modeling tasks.

What Are Conformation Attributes?

Conformation attributes are a part of the attribute space defined specifically for conformation nodes in SAMSON’s Node Specification Language. These attributes allow users to pinpoint and work with specific molecular conformations based on predefined criteria, such as the number of atoms or selection-related properties.

For simplicity, the conformation attribute space is identified as conformation, or its short name co. For example, co.nat is the shorthand for the attribute that corresponds to the number of atoms in a conformation. These attributes can be used in expressions to filter and analyze conformations more effectively.

Inherited Attributes for Conformation Nodes

Conformation nodes inherit some attributes from the node attribute space, which gives modelers flexibility and consistency. Here’s a summary of the most commonly used ones:

  • name (n): Filters conformations based on their names. For instance, co.n "A" matches conformations with the name A, and co.n "L*" addresses names beginning with L.
  • selected: Indicates whether a conformation is currently selected. Example usage includes co.selected or its negation not co.selected.
  • selectionFlag (sf): A boolean attribute to mark specific selections. You can check or unset flags on conformations using co.sf or co.sf false for filtering conformations.

Specific Attributes for Conformations

In addition to the inherited attributes, conformation nodes have their own specific attributes. One particularly useful one is:

  • numberOfAtoms (nat): This attribute allows you to filter conformations based on their total atom count. If you are analyzing a large dataset, this attribute ensures you target only the conformations of interest. For example:
  • co.nat > 100: Finds conformations with more than 100 atoms.
  • co.nat 100:200: Matches conformations with atom counts between 100 and 200.

Such expressions provide a flexible way to handle data and focus on relevant molecular conformations during your workflows.

Learn More

To make the best use of these capabilities, we recommend referring to the official SAMSON documentation page at Conformation Attributes in SAMSON. It contains detailed examples and explanations for every functionality discussed here, ensuring you can fully leverage conformation attributes in SAMSON.

*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.

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