When working on large biomolecular structures, one of the time-consuming tasks in molecular modeling is quickly identifying key residues—like terminal residues or specific charged groups—without manually sifting through hundreds of atoms. Whether you are preparing a structure for dynamics or setting up restraints, knowing how to programmatically select residues with distinct properties can save a lot of time and errors.
This post takes a closer look at residue-level attributes in SAMSON’s Node Specification Language (NSL), focusing on how to filter residues based on structural, chemical, or contextual tags. The goal is simple: give you reusable patterns that help automate tasks like identifying termini, charged residues, or even residues with complete backbones for further analysis.
Why Select by Residue Attributes?
Structures from PDB files often come with incomplete or ambiguous data. You may need to:
- Isolate terminal residues for endpoint constraints
- Select charged residues involved in salt bridges
- Filter out residues with missing atoms or backbones
- Choose only residues with standard naming
Selecting all this manually is slow and error-prone. SAMSON’s NSL lets you use compact expressions to target exactly what you need.
Example: Selecting Terminal Residues
The residue.terminal attribute (r.ter) matches residues that are either N-terminal or C-terminal:
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r.ter |
This query returns all terminal residues. Use this when deciding where to cap proteins or apply end constraints during minimization.
Want all alpha carbons in terminal residues? Try:
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"CA" in r.ter |
This targets atoms by name (“CA”) within terminal residues—great for adding visual markers or restraints.
Example: Residues with Complete Backbones
If you’re modeling peptides and want only residues with a full backbone structure, use:
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r.caab |
This helps discard incomplete residues, which are often problematic during energy minimization or when secondary structure assignment relies on full atom representation.
Example: Charged Residues by Side Chain
Identifying charged residues is especially helpful for calculating pKa shifts or simulating electrostatics:
r.c neg– negatively charged residues (e.g., ASP, GLU)r.c pos– positively charged residues (e.g., LYS, ARG)r.c neu– neutral residuesr.c neu, pos– neutral or positively charged residues
This becomes very powerful when filtering entire sets for interaction detection or pocket analysis.
Combining Conditions
The real strength comes from combining multiple conditions. For example, to select all terminal residues that are also positively charged:
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r.ter and r.c pos |
With these concise expressions, you’ll streamline visualization, restraint definition, or preprocessing steps.
Tip: Start with Short Names
While full attribute names like residue.terminal are supported, short forms make writing queries much quicker. For instance:
r.t HIS– select all histidine residuesr.p polar– all polar residuesr.pI < 6.0– residues with isoelectric point below 6.0
Conclusion
Residue attributes in SAMSON’s Node Specification Language offer a compact and powerful way to filter structural units while modeling. They can help automate tedious selections, reduce manual errors, and speed up repeatable workflows significantly.
Want more examples and a full attribute list? Visit the full documentation page at https://documentation.samson-connect.net/users/latest/nsl/residue/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Discover more and download it at https://www.samson-connect.net.