Whether you’re running simulations, training machine learning models on molecular data, or preparing a paper, molecular modeling projects often involve more than just molecules. You may need Python scripts, research images, datasets, PDFs, and more. Managing all of these scattered files can become frustrating—especially when transferring your work between machines or sharing it with collaborators. SAMSON offers a solution some users may overlook: Universal File Embedding.
With file embedding in SAMSON, your entire project ecosystem—molecules, simulation settings, code, images, publications—can travel together in one self-contained document. Here’s how it works.
Embedding Files and Folders in Documents
In SAMSON, a document is the workspace that contains all your molecular models, simulators, and associated data. Starting from version 2024, SAMSON documents support Universal File Embedding. This means you can drag and drop any file or folder directly into your document.
When you drop a file, you’ll be prompted to choose whether to embed the file—meaning it will be saved within the document—or simply link to its current location. Embedding is the safer choice when you’re working across multiple devices or sharing your project with others.
What Can Be Embedded?
- Python scripts and full Python applications (e.g., ML tools, analysis pipelines)
- Images (e.g., diagrams, molecular renderings)
- PDFs (e.g., supporting papers or notes)
- Text and data files (e.g., parameters, results, spreadsheets)
- Folders containing project-related content
Thanks to this approach, documents become portable and reproducible research packages. You avoid broken links, lost data, and the tedious reassembly of project files. Anyone you share the document with will see exactly what you created, down to that helper script you wrote to analyze hydrogen bonds.
How to Embed Files
There are two main ways to embed files and folders:
- Drag-and-drop one or more files directly into your SAMSON document. You’ll be prompted with an embedding dialog.
- Use the menu: navigate to Home > Embed files or Home > Embed folders.
Once embedded, these files are stored inside the SAMSON document itself and can be accessed or exported later if needed.
Why It Matters for Collaboration
When working in a collaborative team or archiving results for later retrieval, missing input files or forgotten scripts can be a big problem. Embedding solves this neatly. By keeping everything inside a single document, you’re better equipped for reproducibility, easing peer review, or just revisiting a project months later.
Embedded documents can also be published securely via SAMSON Connect, with control over visibility (public, hidden, or restricted access).
Toward Reproducible Molecular Workflows
As research increasingly emphasizes transparency and reproducibility, having your entire workflow embedded in your modeling document is a big step toward cleaner, shareable science. This small feature in SAMSON can save time, prevent errors, and ensure that your collaborators or future self always have the full picture.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.