A molecular model can be full of useful information—and still be awkward to work with. You may need to isolate a ligand, focus on its binding site, change how it is displayed, and then repeat the same sequence later. Remembering commands and searching menus can interrupt the scientific question you were trying to answer.
SAMSON AI offers another way to work: describe certain tasks in natural language, right inside SAMSON. This can be useful when you know what you want to do but do not remember the exact command or selection syntax.
/ in the Assistant input to see available commands.Start with the outcome you want
Open the Assistant from Interface > Assistant, or use Ctrl+0 on Windows and Linux or Cmd+0 on Mac. The commands most useful for hands-on document work are /do and /select, but they serve different purposes.
Use /do when you want SAMSON AI to carry out an action in the document. For example, you could ask it to zoom to a binding site, select a ligand and apply a licorice model, or remove water. A practical sequence might be:
/do select the ligand and apply a licorice model./do zoom to the binding site./do select the gaussian surface and make it light blue.
These examples illustrate a useful habit: describe the object and the intended change plainly. If a request combines several operations and the result is not what you expected, try expressing the task as smaller steps. That makes it easier to see which part needs clarification.
Use selection as a question you can inspect
When the challenge is identifying atoms or structural features, try /select. You can ask for selections such as /select all side chains within 5 angstrom of the ligand. or /select all lysines in chain B. SAMSON AI displays the corresponding Node Specification Language (NSL) query and executes it.
That makes selection useful for more than saving typing: the displayed NSL gives you a chance to inspect how a natural-language request was translated. If the selection is broader or narrower than intended, refine the wording—for example, specify a chain, a distance, or the reference molecule. For an unfamiliar selection, checking the resulting nodes in the document is a sensible step before using that selection in further work.
When a task needs code
For work that is better expressed as a reusable or more customized procedure, use /script. It generates Python scripts that use the SAMSON Python API. Examples from the documentation include translating atoms, creating a small GUI with a distance input and Move button, and computing a receptor’s gyration radius. You can also combine SAMSON’s API with other Python modules, for tasks such as machine learning or trajectory analysis.
Think of the distinction this way: use /do for an action in the current document, /select when the main problem is identifying nodes, and /script when you need Python code for a more tailored task. Generated answers still deserve review; AI responses can be ambiguous or inaccurate, so verify important results rather than treating them as unquestionable.
Bring reference material into the conversation
If your question depends on a document, /learn can read a regular web page or PDF from a URL. You can then ask about the material with /refer. Learned information persists when SAMSON is turned off, until you use /forget, which removes all learned information. This can help keep a document-based question close to the modeling task, though it is worth noting what you have asked the Assistant to learn.
SAMSON AI may collect and store search queries and interactions to improve its services. Messages are encrypted during transmission, but the documentation notes that no electronic transmission or storage method can be guaranteed completely secure. It also cautions that responses may be incomplete, biased, ambiguous, or inaccurate. Keep those limitations in mind, especially when handling sensitive information or relying on an answer for a consequential decision.
The practical takeaway: you do not have to remember every menu path or selection expression before moving forward. State the outcome, choose the command that fits the task, and inspect the result. For command details and further examples, see the SAMSON AI documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.