When working on complex molecular models, it’s common to ask very specific questions about a particular system: How many backbone groups have a partial charge above a certain threshold? Which ones are invisible or lack material? Are there backbones with a specific number of atoms, or unique names?
Answering these questions quickly can be a huge time-saver when preparing simulations, cleaning models, or designing molecules. This is where SAMSON’s Node Specification Language (NSL) and its attribute system becomes particularly helpful.
In this blog post, we’ll explore how to filter molecular backbone structures using their attributes in SAMSON—primarily via the bb prefix (for backbones) and defined attribute short names in the NSL.
What is a backbone in NSL?
In SAMSON, a backbone is a node that represents a structural group at a certain level of abstraction—something commonly encountered in peptides, polymers, or coarse-grained models.
The attributes associated with backbone nodes include both:
- General Node attributes (such as visibility, material, name, etc.)
- Structural Group attributes (such as number of atoms, element counts, formal and partial charge, etc.)
Examples of Useful Queries
Here are some real-world examples that show how to combine these attributes in the NSL syntax to find exactly what you need:
- Backbones with no assigned material:
not bb.hm - Invisible backbones:
not bb.v - Backbones with a partial charge above 1.5:
bb.pc > 1.5 - Backbones with between 10 and 20 carbon atoms:
bb.nC 10:20 - Named backbones (e.g., names starting with ‘L’):
bb.n "L*"
What shortcuts are available?
Many attributes come with short names to streamline queries. For example:
| Attribute | Short Name | Example |
|---|---|---|
| hasMaterial | hm |
bb.hm |
| formalCharge | fc |
bb.fc > 1 |
| numberOfAtoms | nat |
bb.nat 100:200 |
| partialCharge | pc |
bb.pc 1.5:2.0 |
Tips for Effective Searching
- Use ranges: SAMSON accepts syntax like
bb.fc 1:3to specify a value range. - Combine queries: You can refine your search by combining criteria using logical operations like
and,or(see the NSL documentation for more). - Use wildcards in names: For string attributes like
name, wildcards such as*enable flexible matching.
Saving Time During Model Preparation
Whether you’re selecting backbones missing visual information, filtering hydrophobic side chains, or sanitizing partial charge distributions, using NSL queries on backbone attributes can dramatically speed up common molecular modeling tasks in SAMSON.
You can see the full reference list of backbone node attributes available in SAMSON’s Node Specification Language directly in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.