When working with complex biomolecular models, molecular modelers often need to isolate or highlight specific parts of their systems—side chains with a certain number of atoms, a specific charge, or a given elemental composition. This type of selective filtering can be tedious in many platforms, especially for large molecular assemblies.
In SAMSON, the Node Specification Language (NSL) makes this easier. In this post, let’s explore how to use side chain attributes effectively—especially those related to atom counts and physical properties—to quickly select the molecular fragments you’re interested in analyzing or editing.
Why this matters
If you’re modeling proteins, ligands, or materials with repeating subunits, you may want to:
- Identify side chains with high or low formal charges.
- Select side chains with a large number of atoms or specific element types (like carbon or oxygen).
- Find side chains with specific partial charges.
Manually doing this for hundreds or thousands of side chains is obviously error-prone and time-consuming. SAMSON’s NSL lets you express these conditions cleanly using simple rules.
Key attributes for filtering side chains
Here are some useful attributes available in the sideChain (short name sc) attribute space:
sc.nat— total number of atomssc.nC— number of carbon atomssc.nH,sc.nN,sc.nO,sc.nS— number of H, N, O, S atomssc.fc— formal charge of the side chainsc.pc— partial charge
Examples in practice
If you want to select all side chains with more than 8 carbon atoms:
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sc.nC > 8 |
To find side chains with a formal charge of +1 or more:
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sc.fc >= 1 |
To filter side chains with a partial charge in the range 1.2 to 2.0:
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sc.pc 1.2:2.0 |
Want only small side chains with between 10 and 30 atoms?
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sc.nat 10:30 |
You can also combine these. For example, to find side chains rich in oxygen and with a moderate size:
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sc.nO > 5 and sc.nat 30:100 |
Working with coarse-grained atoms
For coarse-grained models, the ncga attribute is helpful. This gives the number of coarse-grained atoms in the side chain:
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sc.ncga < 200 |
Integration into workflows
These queries can be typed directly into SAMSON’s search field or embedded into scripts and workflows, enabling fast iteration in areas like:
- Binding site analysis
- Material design with custom subunits
- Charge balancing for simulation preparation
Conclusion
The ability to target side chains based on structural and electrostatic attributes can save hours of manual work. Once you get familiar with NSL’s concise syntax, tailoring selections becomes both flexible and dependable.
To explore more about the sideChain attribute space in NSL, visit the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/sideChain/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.