A common frustration in molecular modeling is not knowing what you want to do—it is finding the right selection, command, or menu to make it happen. You may want to isolate a ligand, inspect nearby residues, remove waters, or change how a surface is displayed, but each task can involve a different part of the interface.
SAMSON AI offers a practical way to express some of these tasks in natural language. Open it from Interface > Assistant, or use Ctrl+0 on Windows and Linux, or Cmd+0 on Mac. Typing / in the Assistant input shows the available commands.
Start with the selection
Selections are often the first step in a modeling task. Instead of manually navigating a molecular structure, use /select followed by a description of the nodes you want. For example:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
SAMSON AI displays the corresponding Node Specification Language (NSL) for the request and executes it. This is useful not only for getting to a selection, but also for seeing how a plain-language description maps to a structured query. If the result is not what you intended, refine the wording and try again; for important work, inspect the selected nodes before continuing.
Then ask for a document action
Once you have the relevant nodes, /do can request an action in the document. For example, you might ask it to zoom to the binding site, select the ligand and apply a licorice model, or remove water. A request can also combine a selection with a display change, such as selecting a Gaussian surface and making it light blue.
A useful habit is to make the task specific: name the object or region, then state the intended action. That gives you a clear way to check the result. For instance, you can first request a binding-site selection, review it, and then ask to zoom to that site. Breaking a task into visible steps makes it easier to catch an incorrect selection before it affects later work.
When a command is not enough
For tasks that need custom logic, /script generates Python scripts that use the SAMSON Python API to interact with the document. The documentation gives examples such as translating all atoms in the z direction by 1 angstrom, creating a small GUI for entering a distance, or computing the gyration radius of a receptor. This route is better suited to repeatable or specialized operations than a one-off visual adjustment.
Whether you use a natural-language command or a generated script, treat the result as something to review. SAMSON AI can misinterpret a request or provide inaccurate information. Keep queries clear, check selections and changes in the document, and verify critical scientific results independently.
A simple workflow to try
- Open the Assistant and type
/to see the commands. - Use
/selectto identify the molecular region you want to work with. - Inspect the selection, then use
/dofor a document action such as zooming, changing a representation, or removing water. - Use
/scriptwhen the task calls for custom Python logic.
This approach can reduce the friction between a modeling question and the corresponding operation, while keeping the modeler involved in checking what actually happened. For command details, limitations, and privacy information, see the SAMSON AI documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.