When working on large biomolecules, modelers often need to focus on specific structural features of side chains—whether to study interaction sites, assess functional groups, or prep for simulations. One common challenge is identifying side chains based on their atomic composition. Imagine needing all side chains with more than 10 hydrogen atoms, or filtering out those that contain sulfur. In SAMSON, this can be done efficiently using the Node Specification Language (NSL).
The sideChain attribute space, with short name s or sc, gives detailed access to attributes of side chain nodes in the molecular model. These attributes are inherited from two other attribute spaces—node and structuralGroup. Among the most useful for composition-based filtering:
sc.nC— number of carbon atomssc.nH— number of hydrogen atomssc.nN— number of nitrogen atomssc.nO— number of oxygen atomssc.nS— number of sulfur atomssc.fc— formal chargesc.pc— partial charge (a float)
Here are a few practical examples you might find useful:
1. Find side chains with a high number of hydrogens
sc.nH > 10 — Selects all side chains with more than 10 hydrogen atoms. Useful when studying hydrophobic pockets or considering hydrogen-based interactions.
2. Filter side chains without sulfur atoms
sc.nS 0 — Filters out all sulfur-containing side chains. Especially helpful when sulfur artifacts or reactive properties are to be excluded.
3. Narrow down to aromatic or polar residues
You might use a combination, such as:
sc.nC > 6 and sc.nO > 2, to detect potentially aromatic and polar side chains (such as tyrosine).
4. Inspect formal charges
sc.fc != 0 — A quick selection for all ionized side chains, helping with electrostatic surface inspections or when setting up QM regions.
Shortcuts and ranges
Ranges can be specified using colons. For instance, sc.nH 5:10 selects side chains with between 5 and 10 hydrogens (inclusive). Negative comparisons can be constructed using not, such as not sc.nO (amt > 0 assumed).
This approach offers a precise way to identify and manipulate molecular groups of interest, all from the selection bar within SAMSON. If you’re scripting or automating workflows, these NSL filters can be set programmatically.
To summarize, knowing how to filter side chains by atomic composition in SAMSON using NSL speeds up analysis and enables rigorous model preparation. This proves especially valuable when configuring large molecular systems or pinpointing candidates for functional studies.
To discover more selection options and attribute combinations, you can check the full documentation on side chain attributes here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.