When working with complex biomolecular models, isolating specific backbones based on their atomic composition can be an important step in analyzing or preparing systems for simulation or visualization. Whether you’re trying to identify coarse-grained models, locate structurally diverse backbones, or clean up your model before exporting, manually navigating large molecular assemblies can be time-consuming. Fortunately, the Node Specification Language (NSL) in SAMSON offers a set of backbone attributes that make this filtering straightforward and precise.
What are backbone attributes?
In SAMSON, backbone elements refer to structural group nodes used to represent the backbone of molecular systems. The NSL lets you specify filters and queries on these nodes using attributes such as number of atoms, carbons, hydrogens, and so on. These properties are especially useful when dealing with heterogeneous systems such as proteins with ligands or polymers with embedded atoms.
Examples of useful filters
Say you want to select all backbone nodes with fewer than 100 atoms—potentially indicating peptide fragments or smaller structural groups. You can use:
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bb.nat < 100 |
If you’re focusing on hydrogen content, perhaps to identify backbone groups that may participate in hydrogen bonding or those that were coarse-grained improperly, try:
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bb.nH > 10 |
You can also combine filters to refine your searches further. For example, to select backbone nodes with between 100 and 200 atoms and fewer than 10 nitrogens, use:
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bb.nat 100:200 and bb.nN < 10 |
Why atomic composition filtering matters
Filtering by atomic makeup is not just about sorting through structures—it helps you make sense of noise in your model. Here are a few practical reasons this is useful:
- Cleanup and optimization: Identify unusual or incomplete backbone groups before exporting or simulating your system.
- Model consistency: Spot coarse-grained backbones in all-atom simulations using
bb.ncga, the number of coarse-grained atoms. - Diagnostics: Find backbones with high formal charges or unexpected partial charges that could ruin your simulation.
A closer look at the available attributes
The following are some key attributes you can specify for backbones:
bb.nat: Total number of atomsbb.nC: Number of carbon atomsbb.nH: Number of hydrogen atomsbb.nN: Number of nitrogen atomsbb.nO: Number of oxygen atomsbb.nS: Number of sulfur atomsbb.fc: Formal charge (integer)bb.pc: Partial charge (floating-point)bb.ncga: Number of coarse-grained atoms
These attributes allow you to build precise selection expressions, making your modeling workflow in SAMSON more efficient.
Learn more
Mastering these attributes can save time and give you better control over your models. To explore all available attributes and their syntax in the Node Specification Language, visit the official SAMSON documentation:
https://documentation.samson-connect.net/users/latest/nsl/backbone/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.