Working with molecular structures often means managing complex selections—atoms, residues, chains, or interaction regions. For many researchers, this translates into repetitive interface navigation, complex queries using atom specifications, or scripting with a steep learning curve.
But what if you could simply describe what you want to select, and let your software do the rest?
With the /select command in SAMSON AI, you can do just that. Trained to interpret natural language, SAMSON AI allows users to select parts of a molecular system without writing a single line of code—or even knowing selection syntax.
Why this solves a real problem
Many molecular modelers struggle with selecting exactly the right atoms or residues, especially in large systems. Imagine trying to highlight:
- All side chains within a certain distance from a ligand
- All lysines in a specific chain
- Just the binding site
Traditionally, this might involve learning a specific selection language (e.g., VMD’s atom selections) or writing conditional scripts. The /select command removes that overhead. You write what you mean. SAMSON selects it for you.
How it works
In SAMSON AI, simply type natural language commands prefixed with /select. Some examples from the documentation include:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
SAMSON AI will interpret your query, convert it into SAMSON’s Node Specification Language (NSL), and execute the corresponding selection in the molecular document.
This makes it especially helpful when exploring unfamiliar structures, preparing for analysis, or simply saving time for common visualization tasks. Because it’s powered by GPT-5 (in the Professional Plan), the assistant interprets queries with considerable flexibility.
When it really shines
We’ve found the /select command particularly useful when combined with visualization or analysis steps. For example:
- Select a binding site, then generate a surface visualization.
- Select atoms near a ligand before computing interaction energies.
- Prepare selection subsets for dynamic simulation runs.
Rather than navigating through trees or watching video tutorials to understand selection syntax, you’re interacting directly with your assistant.
And best of all, you can explore the selection logic by seeing how SAMSON AI translated your input into NSL, giving you transparency and flexibility to adjust or reuse the selection later.
Want to try it?
You can open SAMSON AI through Interface > Assistant or by using the shortcut Ctrl + 0 on Windows/Linux, or Cmd + 0 on Mac.
The assistant will display available commands when you type /, including /select.
If you often spend time selecting molecular regions, this may be a small change with big returns in your workflow. It’s intuitive, fast, and reduces your cognitive overhead when navigating complex structures.
To learn more about what /select can do and how it interacts with other commands, visit the SAMSON AI documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net