From Folder Clutter to Useful Candidates: Filter Structures by What’s Inside

A molecular project can quickly accumulate folders containing structures of very different sizes and compositions. When you need to find a particular subset—large systems, folders with several chains, or structures with a specific total charge—opening folders one by one is tedious. SAMSON’s Node Specification Language (NSL) lets you search folder nodes by these properties.

The key is to choose a measurement that reflects the question you are trying to answer. Folder attributes use the f prefix, and they match folder nodes. For example, f.nat refers to the number of atoms, while f.nc refers to the number of chains. You can use a full attribute name or its short form.

Start with the size of the structure

If you are looking for folders containing larger structures, filter by atom count. The query f.nat > 100 matches folders whose structures have more than 100 atoms. To focus on a size band instead, use f.nat 100:200.

This is useful when a project contains structures at several scales and you want to locate folders in a particular range. The same pattern applies to counts of specific atoms: f.nC < 10 looks for fewer than 10 carbon atoms, and f.nH 10:20 searches for a hydrogen count between 10 and 20. Other available composition attributes include nitrogen (f.nN), oxygen (f.nO), and sulfur (f.nS).

Use structural counts to narrow the search

Atom count is not always the most useful measure. If you are sorting folders by how a structure is organized, try the number of chains, molecules, residues, or segments. For instance, f.nc < 3 matches folders with fewer than three chains, while f.nm 2:4 targets folders with between two and four molecules. To find folders with more than 100 residues, use f.nr > 100.

There are also attributes for coarse-grained atoms, structural groups, and structural models. Their short names are f.ncga, f.nsg, and f.nsm. For example, f.nsm > 4 searches for folders with more than four structural models. These counts can help distinguish folders by the kind of structural content they contain, rather than by overall atom count alone.

Search by total charge

When charge is the important property, use f.fc for formal charge or f.pc for partial charge. The query f.fc 6:8 matches folders with structures whose total formal charge is between 6 and 8. For total partial charge, f.pc 1.5:2.0 selects folders in that range. These attributes answer different questions, so choose the one that corresponds to the charge information you need.

A practical way to build a search

  1. Decide what you need to distinguish: size, composition, structural organization, or total charge.

  2. Choose the matching attribute—for example, f.nat for atom count or f.nr for residue count.

  3. Use a comparison such as > 100 or a range such as 100:200, depending on whether you have a cutoff or a target interval.

  4. Adjust the threshold or range if the results are broader or narrower than you need.

Working through one criterion at a time helps make a search easier to understand and refine. Folder attributes also inherit several general node properties, including visibility, selection, and name; the folder reference lists those alongside the structure-specific counts.

For the complete attribute list and more examples, see the SAMSON folder attributes reference.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

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