From “Where’s That Command?” to a Clearer Molecular Modeling Workflow

A familiar interruption in molecular modeling is not always a difficult scientific question. Sometimes it is the small task that breaks your concentration: finding the right command, selecting a particular group of atoms, changing a representation, or repeating a few steps just to inspect a structure. SAMSON AI can help with these in-application tasks by accepting natural-language requests and, when appropriate, carrying them out in the document.

The useful idea is to treat the assistant as a way to shorten the distance between what you want to do and the tool that does it. You can open it from Interface > Assistant, or use Ctrl+0 on Windows and Linux or Cmd+0 on Mac. The commands below offer different levels of control, from asking for an action to generating a script you can inspect.

Use natural language for a document action

When you know the outcome you want but do not remember where the relevant command lives, use /do. For example, you can ask SAMSON AI to zoom to a binding site, remove water, erase surfaces, or select a ligand and apply a licorice model. These requests are aimed at performing actions in the current document.

A practical habit is to make each request specific and focused. Instead of combining several unrelated changes into one instruction, try one action at a time. You can then check the document before moving on. That makes it easier to spot a misunderstanding, especially when an action changes a visualization or removes content. The documentation notes that AI responses can be inaccurate or misinterpret a request, so review the result rather than assuming every action was carried out as intended.

Make selections easier to describe

Atom and residue selection can involve precise criteria that are awkward to express through repeated interface steps. With /select, you can describe the target in ordinary language. Examples include selecting the binding site, lysines in chain B, or side chains within 5 angstrom of the ligand.

SAMSON AI displays the corresponding Node Specification Language (NSL) query and executes it. That is useful in two ways: it can save time when forming a selection, and it gives you a query to inspect when you want to understand how the selection was specified. For instance, if the result is broader or narrower than expected, the displayed NSL can help you examine the selection criteria instead of treating the result as a black box.

Use scripts when the task needs more structure

Some jobs are better expressed as a short program than as a one-off action. The /script command generates Python scripts that use the SAMSON Python API to interact with the document. Examples from the documentation include translating all atoms in the z direction by 1 angstrom, creating a small GUI with a distance input and a Move button, and computing the receptor’s radius of gyration.

This can be a useful starting point when a task has several steps or when you want to adapt an operation for later use. Generated code should still be reviewed and tested in the context of your document, particularly before applying changes to a structure. For more information about the API, see the SAMSON scripting documentation.

A simple workflow to try

1. Open the Assistant and state the modeling task in a short, concrete request.
2. Use /select when the main challenge is identifying the right nodes; inspect the displayed NSL query and the resulting selection.
3. Use /do for a direct document action, then check the outcome in the workspace.
4. Use /script when you need a more involved or customizable operation, and review the generated Python before relying on it.

SAMSON AI is based on GPT-5 in the Professional plan. As with other AI tools, it may lack recent information, misunderstand ambiguous requests, or produce inaccurate answers. Treat it as an assistant for navigating and carrying out work—not as a substitute for checking scientific results or validating important changes.

To explore the commands and their examples, read the SAMSON AI documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.