Modeling biomolecules efficiently often comes down to how well you can find and select components based on your needs. If you’ve ever needed to isolate side chains with a certain number of atoms, a specific formal charge, or unique visibility properties, then you know that clicking through a 3D structure manually can be time-consuming.
The Node Specification Language (NSL) in SAMSON offers a much faster and more precise way to do this. Specifically, attributes available in the sideChain attribute space give you powerful tools to target just the structural items you’re interested in.
Why is this useful?
Suppose you’re working with a complex protein and want to:
- Find all side chains with more than 8 carbon atoms (possibly hydrophobic residues)
- Identify side chains with a formal charge greater than +1
- Hide or make visible a subset of the molecule based on properties
Instead of relying on labor-intensive manual selections or writing scripts, you can use NSL queries like:
|
1 2 3 |
sc.nC > 8 sc.fc > 1 not sc.v |
Exploring Side Chain Attributes
NSL allows querying using both full attribute names and short names. Here are some useful attributes specific to side chains:
sc.n— name of the structural group (pattern matching allowed)sc.fc— formal charge (integer)sc.nat— number of atomssc.nC,sc.nH,sc.nN,sc.nO,sc.nS— number of specific atomssc.pc— partial charge (real number)sc.v— visible (boolean)sc.selected— is the side chain currently selected?
You can combine filters to create more advanced queries. For example, to select side chains that are visible, have more than 10 atoms and a partial charge above 1.0:
|
1 |
sc.v and sc.nat > 10 and sc.pc > 1.0 |
Working with Materials and Visibility
If part of your workflow involves material properties, you can find side chains that own or just have material assignments:
|
1 2 |
sc.hm # has material sc.om # owns material |
You can also filter by selection or visibility flags:
|
1 2 |
sc.vf # visibility flag sc.sf # selection flag |
This is especially useful when you build up complex selection sets, e.g. hiding non-relevant parts or color-coding based on charge or composition.
Real-World Use Cases
- Preparation for simulations: Select charged side chains to adjust protonation states or ion placements.
- Visualization: Hide non-relevant residues, or highlight regions with unusual partial charges.
- Mutation planning: Identify large side chains and plan space accommodations for substitutions.
For anyone working with molecular systems that include proteins, nucleic acids, or polymers, mastering these attributes can save hours during model building, analysis, and presentation.
To explore all available side chain attributes and their usage, visit the full documentation: 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