A molecular project can look complete on your computer and still be difficult for someone else to continue. The model may be accompanied by analysis scripts, input files, notes, or a small Python app—but if those pieces are scattered across folders or separated from the document, a colleague has to reconstruct how they fit together. That costs time and makes it harder to repeat the workflow.
SAMSON documents can hold more than molecular models: they can embed Python scripts, files, and folders. This offers a practical way to keep project materials together when you share a workflow. It does not remove every setup requirement, but it can make the handoff much clearer.
Build the workflow before you share it
Start by developing and checking the script in SAMSON. The integrated Python Console is useful for trying commands and automating tasks interactively. For a script you want to save and run again, use the Code Editor, which can open and modify Python files and run them. It includes syntax highlighting and auto-completion, and SAMSON provides Python templates that can help you get started with the SAMSON Python API.
If you are repeating a task you normally perform through the interface, look for its Python equivalent before writing everything from scratch. For example, SAMSON can show Python code for certain commands, color palettes, and visual presets. Copying that code into the editor or console can turn a familiar interface action into a useful starting point for a script.
Then test the workflow in the context in which it will be used. Check that it operates on the intended molecular document and that the files it needs are available. If it relies on additional Python packages, review them in the Python Package Manager, opened from Python Console > Edit > Manage packages…. The manager installs packages using pip and can display installed package versions. For a handoff, it is helpful to note the package names and any required versions in the project notes; embedding a script should not be mistaken for automatically packaging its Python environment.
Keep the supporting files with the document
Once the materials are ready, drag files or folders into SAMSON and choose to embed them when prompted. You can also use Home > Embed files or Home > Embed folders. Embedded items are stored within the document, making it self-contained with respect to those files and folders.
Consider including the scripts and data needed to understand the project, along with a short note explaining what each script does and how to start. If a script depends on a package that is not part of the standard setup, say so explicitly and identify the package and version. Clear notes help the next person distinguish the materials stored in the document from anything they may need to install separately.
To inspect an embedded Python script, double-click it to open it in the Code Editor. From there, a user can review or run the script. The Python Console is also available for quick execution. Keeping the instructions close to the files makes it easier for a colleague, student, or future version of you to find the intended entry point.
Make the handoff understandable
Before sharing, ask a simple question: could someone who did not create this project identify the model, the script to start with, and any external setup they need? A concise README or project note can answer that without turning the document into a full manual. Mention the purpose of the workflow, the expected input, and what the script changes or produces. For workflows still in development, editable local packages are available through the Package Manager, but SAMSON notes that editable installs may need attention on some macOS installations after restarting.
You can distribute a SAMSON document by email, GitHub, or through SAMSON Connect Documents. The recipient can open the document and access its embedded materials. This approach is useful for sharing a research analysis, a teaching exercise, or a project handoff where the molecular model and its supporting files belong together.
The goal is not simply to attach more files. It is to make the next action clear and to reduce the number of details a collaborator must recover from memory. For guidance on the Python environment, package management, the Code Editor, and embedding, see the SAMSON Scripting documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.