Quickly Identifying Molecular Folders With Specific Structures in SAMSON

Modeling complex molecular systems often involves navigating through large, layered hierarchies of folders in your design environment. If you’ve ever found yourself digging through countless folders in SAMSON trying to locate a structure with precisely 100 to 200 atoms or containing exactly 3 chains, you’re not alone. Many researchers and designers working at scale face the same challenge: filtering and selecting specific types of molecular folders in seconds.

Fortunately, SAMSON’s Node Specification Language (NSL) provides a powerful and concise way to filter content, particularly folder nodes. In this blog post, we’ll focus on how to take advantage of folder attributes to streamline your selection and filtering workflows.

What Are Folder Attributes?

Folder attributes in NSL are special keywords that can be used to query properties of folder nodes — that is, folders that contain molecular structures or other elements.

NSL uses a prefix f. or the longer form folder. to reference folder attribute space. For example, to find all folders that contain more than 100 atoms, you simply write:

This is shorthand for:

Common Folder Attribute Filters

Here are a few practical filters you can use in SAMSON:

  • Filter by number of atoms:
    f.nat 100:200 — selects folders with 100 to 200 atoms.
  • Filter by number of chains:
    f.nc < 3 — shows folders with less than 3 chains.
  • Filter by molecular count:
    f.nm 2:4 — folders with 2 to 4 molecules inside.
  • Filter by visibility:
    f.v true — only the folders that are currently visible.

More Specific Queries

Need to find folders containing molecules rich in specific atoms? No problem. Try these:

  • f.nC > 5 — folders with more than five carbon atoms.
  • f.nO 2:4 — folders containing 2 to 4 oxygen atoms.
  • f.fc 1 — folders with a total formal charge of +1.
  • f.pc 1.5:2.0 — folders with partial charges in that range.

Similarly, you can use not to exclude results. For instance, not f.h will exclude hidden folders from your selection.

Use Case Example

Imagine working with dozens of candidate molecular designs and needing to evaluate only the ones with more than 130 residues. Instead of manually inspecting each, simply run:

This saves time and reduces errors, particularly in large projects.

Conclusion

Using folder attributes in SAMSON’s NSL can significantly streamline molecular modeling workflows by allowing direct, expressive queries for the types of molecular data you’re working with. This helps keep your design space organized and responsive, especially when working at scale.

To learn more about folder attributes and other advanced queries, visit the full documentation: https://documentation.samson-connect.net/users/latest/nsl/folder/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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