A familiar frustration in molecular modeling is knowing what you want to do but having to remember where the right command, menu, selection rule, or editor lives. A small task—selecting a ligand, changing its representation, and focusing the view—can turn into a sequence of interface steps. SAMSON AI offers another route: describe the task in natural language, then use the command that best fits the work.
The useful distinction is between acting on the current document, selecting precisely, and creating a reusable script. Choosing the right mode makes a request easier to check and helps keep a quick interaction from becoming an opaque workflow.
Start with a focused action
Use /do when you want SAMSON AI to perform an action in the open document. For example, you can ask it to zoom to a binding site, remove water, erase surfaces, or select a ligand and apply a licorice model. The key advantage is that you can express the goal rather than search through menus for every step.
For a more reliable interaction, phrase one clear action at a time. Instead of combining several changes into a long instruction, try a short sequence: first select the ligand and apply the representation you want; then ask to zoom to the relevant site. This makes it easier to notice whether each result matches your intention before moving on.
/ in the Assistant input to see the available commands.Make selection criteria explicit
Selection is often where an otherwise simple modeling task becomes error-prone. A vague request such as “select the nearby residues” leaves room for interpretation. With /select, describe the target and the criterion you care about—for example, /select all side chains within 5 angstrom of the ligand. You can also ask for a binding site or for all lysines in a named chain.
SAMSON AI displays the corresponding Node Specification Language (NSL) query and executes it. That gives you a useful checkpoint: inspect the selection rule as well as the resulting nodes. If the selection is not what you intended, refine the wording or the criterion before applying a visual or structural change to it.
Use scripts when the task should be repeatable
Some jobs are better expressed as a script than as a one-off action. Use /script to generate Python code that interacts with the document through the SAMSON Python API. Examples include translating atoms in a specified direction, calculating a receptor’s gyration radius, or creating a small GUI with a distance input and a Move button.
A practical rule of thumb: use /do for an immediate document action, /select when the main challenge is defining which nodes to target, and /script when you want code that can support a more customized or repeatable task. Generated scripts can be reviewed and adapted, and the documentation also describes combining the API with other Python modules for work such as trajectory analysis or machine learning.
Bring reference material into the conversation
When your question depends on a specific document, paper, or webpage, /learn can load information from a URL; the documented supported sources are regular web pages and PDFs. Then use /refer to ask questions about the information you provided. This can be helpful when you want to ask targeted questions without repeatedly searching through a long source yourself. Use /forget to clear all learned information; according to the documentation, learned data otherwise persists when SAMSON is turned off.
Keep a scientist’s review in the loop
Natural-language instructions can be ambiguous, and AI responses may be inaccurate or incomplete. Treat the assistant as a way to express and carry out a task—not as a substitute for checking the result. Verify selections, inspect document changes, and review generated code before relying on it, especially when an operation affects many nodes or informs scientific conclusions.
You can open SAMSON AI from Interface > Assistant, or use Ctrl+0 on Windows and Linux and Cmd+0 on Mac. For command details and limitations, see the SAMSON AI documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.