When working on detailed structural analysis or drug design projects, molecular modelers often need to select and manipulate side chains based on specific features — such as the number of atoms or presence of certain elements. This can be time-consuming if done manually, especially in large biomolecular structures. Fortunately, SAMSON’s Node Specification Language (NSL) provides a way to quickly filter side chains based on their attributes.
In this post, we’ll help you become more efficient by showing you how to use NSL to select side chains according to their atomic composition. Whether you’re investigating the polarity of amino acids or optimizing interaction potentials, this can be a simple but powerful tool in your workflow.
Working with Side Chain Attributes
In NSL, side chains have their own attribute space, accessible via the sideChain (or sc) prefix. Many of the attributes useful for selection are numerical and relate to atomic counts:
sc.nat: Number of atomssc.nC: Number of carbon atomssc.nH: Number of hydrogen atomssc.nO: Number of oxygen atomssc.nN: Number of nitrogen atomssc.nS: Number of sulfur atomssc.fc: Formal chargesc.pc: Partial charge
The syntax is intuitive and allows for ranges and comparisons. For example:
|
1 |
sc.nC > 5 |
Selects side chains with more than 5 carbon atoms.
|
1 |
sc.nO 3:6 |
Selects side chains with 3 to 6 oxygen atoms.
|
1 |
sc.fc 1 |
Selects side chains with a formal charge of +1.
Why This Matters
Let’s say you’re screening protein-ligand interactions and looking to identify charged side chains with significant electronegative components. You could isolate side chains with the following query:
|
1 |
sc.fc > 0 and sc.nO > 2 |
This would quickly highlight positively charged side chains rich in oxygen atoms — possibly indicating functional groups participating in hydrogen bonding or ionic interactions.
Or maybe you’re analyzing the hydrophobic core of a protein. In that case, you could use:
|
1 |
sc.nC > 6 and sc.nO 0 |
To identify bulky non-polar side chains with high carbon content and no oxygen.
This ability to concisely specify side chains using NSL dramatically reduces the need for manual selection and helps focus analysis on regions of interest in complex molecular assemblies.
More Examples
Some more quick examples to get you started:
sc.fc -1: Negatively charged side chainssc.nH 10:15: Side chains with mid-range hydrogen contentsc.pc > 0.5: Side chains with significant partial charge
These combinations can be extended further by combining them with other NSL filters based on names, visibility, or material properties.
To learn more and see the full list of available attributes, visit the side chain attribute documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.