One of the persistent challenges in molecular modeling and computational chemistry is staying organized. When molecular projects involve not only structures but also scripts, papers, datasets, and other types of files, managing and sharing all of these assets can become messy. External folders, scattered dependencies, and file version mismatches often slow down collaboration and reproducibility.
What if your molecular document could center and store everything you need? With SAMSON, this is possible through its Universal File Embedding functionality. This feature allows molecular modelers to embed Python scripts, entire folders, datasets, papers, and more—directly inside their modeling documents.
Why File Embedding Matters
Whether you’re writing a simulation script, referencing a research paper, or storing experimental data, linking external files can lead to issues down the line, especially when projects are transferred between machines or collaborators. Embedded files prevent this problem because everything becomes self-contained—it travels with the document.
Use cases include:
- Storing preprocessing or analysis scripts written in Python
- Embedding supplementary images for reports or presentations
- Including configuration files for simulations or visualizations
- Packaging full academic papers directly within your molecular document
How It Works
To embed files or folders into a SAMSON document, simply:
- Drag-and-drop the file or folder into the SAMSON interface. You’ll be prompted to embed it.
- Or, you can use the menu: Home > Embed files or Home > Embed folders.
Once embedded, the file or folder becomes part of the document and stays there until you remove it. Unlike shortcuts or references, it’s the actual content that is preserved inside the document file.
Sharing & Reproducibility
By embedding all needed components of a project into a SAMSON document, collaborators who open it will see exactly what you saw, including any embedded scripts or data. It simplifies reproducibility, a pressing concern in computational science today. No additional files to send, no extra instructions necessary—just one document with everything inside.
Key Advantages
- Portability: Move or share your document without breaking file paths.
- Simplicity: Everything is in one place—no external folders required.
- Archiving: Make project files durable and easier to revisit later on, months or years later.
Whether you’re working on a research article, simulation study, or collaborative molecular analysis, embedding your files can save time and prevent errors. It also makes SAMSON projects a convenient way to archive and share complex modeling workflows.
To learn more about loading molecules and working with embedded files in SAMSON, visit the official documentation: https://documentation.samson-connect.net/users/latest/loading-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.