A crowded molecular project can make a simple question surprisingly time-consuming: which folders contain the kind of structures I need? You may be looking for a small set of chains, a particular range of residue counts, or structures with a specific elemental composition. Checking folders one by one is tedious. SAMSON’s Node Specification Language (NSL) lets you describe folder-level properties and find matching folders with compact expressions.
The key distinction is that these are folder attributes. The folder attribute space, abbreviated f, matches folder nodes. Its count and charge attributes describe structures in those folders, so they can help you narrow a search before focusing on individual structures.
Start with the size of the structure
If you need to separate small systems from larger ones, try the number-of-atoms attribute. For example, f.nat < 1000 matches folders whose structures have fewer than 1,000 atoms. To look within a range, use f.nat 100:200. These are examples, not universal cutoffs: choose values that make sense for your project.
Residue counts can be more useful when you are organizing biomolecular structures. For example, f.nr > 130 selects folders with more than 130 residues, while f.nr 100:130 targets the documented range from 100 to 130. If your first pass returns too many or too few candidates, adjust the values and search again.
Use composition to refine the shortlist
Total atom count does not tell you what a structure contains. Folder attributes also provide counts for carbon, hydrogen, nitrogen, oxygen, and sulfur atoms. For instance, f.nC < 10 matches folders with fewer than 10 carbon atoms, and f.nO 10:20 matches folders with 10 to 20 oxygen atoms. The same pattern applies to the other element-count attributes: f.nH, f.nN, and f.nS.
This gives you a practical way to distinguish structures that have similar overall sizes but different elemental profiles. Treat each expression as a targeted question about a folder, and use the results to decide what to inspect next.
Check organization and charge
Some searches are about how structures are organized rather than their atom counts. Use f.nc < 3 to find folders with fewer than three chains, or f.nm 2:4 to match folders with two to four molecules. Other available counts include segments (f.ns), structural groups (f.nsg), structural models (f.nsm), and coarse-grained atoms (f.ncga).
When charge matters, distinguish formal charge from partial charge. For example, f.fc 6:8 searches for folders whose structures have a total formal charge in the stated range. f.pc 1.5:2.0 uses total partial charge instead. These attributes answer different questions, so select the one that matches the property you are investigating.
Remember names and visibility
Folder attributes also include inherited node properties. You can search by name, as in f.n "A", or use a wildcard-style example such as f.n "L*". Visibility and selection-related attributes are available too: examples include f.v for visible folders and f.selected for selected folders. The inherited selected attribute has no short name in the folder attribute space; use its full form.
A useful approach is to begin with the property that most sharply describes your goal—size, composition, organization, charge, or name—then refine your search with other criteria as needed. The attribute reference lists the available names, short forms, and examples; check it when you need an exact expression or want to explore another folder property.
Read the folder attributes reference to learn more.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.