If you’ve spent time setting up molecular systems in a modeling environment, you know how tedious it can be to select atoms, residues, or chains — especially when you’re working with large biomolecular complexes. Writing specific selection scripts or navigating cumbersome GUIs can break your workflow and slow you down.
What if you could just… type what you want?
This is where SAMSON AI’s natural language selection comes in. Using the /select command in SAMSON AI, you can describe what you want in plain English, and SAMSON AI will perform the selection for you. This shortens your setup time and makes molecular selection more intuitive, especially for users who aren’t scripting experts.
Why Natural Language Selection Matters
In traditional modeling platforms, selecting groups of atoms often involves manually clicking structures, using chain/residue IDs, or crafting complex selection strings. For example, choosing “all lysines in chain B within 5 Å of the ligand” might take multiple steps and require scripting knowledge.
SAMSON AI abstracts this away. It translates natural language into its Node Specification Language (NSL), automatically generating and executing the correct selection command for you.
Examples You Can Use
To use natural language selection, simply open SAMSON AI via the Interface > Assistant menu or press Ctrl+0 (Windows/Linux) or Cmd+0 (Mac). Then type one of the following commands:
/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 and highlight the appropriate nodes. It also displays the underlying NSL query it generated, which is helpful if you want to learn how these selections are represented internally.
Benefits for Your Workflow
This natural language interface makes it easier and faster to:
- Set up simulation regions
- Prepare systems for editing or export
- Perform targeted modifications (e.g. coloring, hiding, analyzing)
Even experienced users benefit from the speed of typing a simple phrase instead of crafting complex selection statements. Meanwhile, newcomers to molecular modeling can focus on scientific questions instead of command syntax.
Bonus: Learn the Language as You Go
Each time SAMSON AI processes a /select query, you get to see the equivalent NSL string. This provides a gentle, low-pressure introduction to scripting selections manually, in case you want to fine-tune them later.
Want to Explore More?
Natural language selection is just one of many SAMSON AI capabilities. You can also execute commands, generate Python scripts, and even teach SAMSON AI to answer questions about documents you give it. But if you’re looking for an immediate productivity boost in model preparation, trying out /select might be the easiest place to start.
To learn more about the /select command and others like it, visit the full documentation page: https://documentation.samson-connect.net/users/latest/samson-ai/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.