When working with large and complex molecular systems, modelers often face the challenge of isolating meaningful subsets of data within a structure. Whether it’s identifying loops in protein backbones or analyzing particular conformational changes, precise selection is essential. Thankfully, SAMSON’s Node Specification Language (NSL) provides powerful filtering capabilities, especially when working with molecular paths.
In this post, we’ll explore how to leverage the path attribute space in NSL to filter molecular paths based on characteristics like atom count, selection state, and more. These tools can help you focus only on the regions of interest—saving you time and making your analyses more manageable.
What is a “path” in SAMSON?
In SAMSON, a path typically specifies a connected sequence of atoms or structural elements—like segments of polymers or chains in proteins. Filtering based on path attributes lets you isolate features like large flexible loops, short segments of ligands, or specific conformational states.
Using the path Attribute Space
The path attribute space (or its shorthand p) allows you to navigate conformation nodes with specialized filters. You can use several attributes in this context:
p.n(name): matches paths by their name, using quoted strings or wildcards.p.selected: identifies paths that are currently selected.p.sf(selection flag): similar toselected, for more advanced control.p.nat(number of atoms): filters paths based on how many atoms they contain.
Filtering Paths by Number of Atoms
If you’re only interested in larger or smaller molecular fragments, p.nat is a useful attribute. For example:
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p.nat > 100 |
This selects paths that contain more than 100 atoms—helpful if you’re trying to find longer chains or flexible components in large molecules.
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p.nat 100:200 |
This filters paths to those with an atom count ranging from 100 to 200. This can be effectively used when screening for medium-sized substructures across different molecules.
Combining Filters for More Precision
Filters can be combined with Boolean logic to narrow down your selections. Here are two practical examples:
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p.nat > 150 and p.selected |
This selects paths with more than 150 atoms and that are currently marked as selected. Useful when refining previous manual selections with numerical constraints.
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p.n "Loop*" and not p.sf |
Selects paths whose names start with “Loop” but are not flagged for selection. A good way to isolate specific residues you may want to edit or analyze further.
Why This Matters
Whether you’re studying molecular flexibility, targeting drug binding pockets, or preparing structural animations, these filters save time and help focus on the parts that matter. Instead of visual scanning or creating scripts, NSL gives you elegant, readable expressions to rapidly get what you need.
To learn more about different path attributes and how to use them, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/path/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.