One constant challenge in molecular modeling is project portability. Whether you’re collaborating with colleagues, moving projects across machines, or preparing simulations for publication, keeping everything together can be frustrating. Files often get separated, paths break, or dependencies go missing. Fortunately, SAMSON provides a powerful way to make your molecular modeling projects self-contained: embedding files and folders directly into documents.
In this blog post, we’ll explore how you can use embedded files and folders in SAMSON to keep everything in one place. From molecular structures and scripts to images and data files, embedding ensures your computational work moves with you – no broken links, no missing files.
Why embed files into SAMSON documents?
When you embed content into your SAMSON document, you’re essentially turning it into a portable archive. This has multiple benefits:
- ✔️ You can move entire projects between computers without worrying about missing files.
- ✔️ You can organize scripts, notes, and auxiliary documents together with your molecular data.
- ✔️ You ensure consistency when sharing with colleagues or archiving projects.
What can be embedded?
You can embed nearly any type of file, including:
- PDFs (e.g., experimental protocols, papers)
- Images (e.g., figures, diagrams)
- CSV or other data files
- Structure files (PDB, MOL2, etc.)
- Python scripts
Folders allow you to structure these embedded files, grouping related content together meaningfully.
How to create folders in your document
To create a folder that organizes your document:
- Click Edit > Folder in the main menu.
- Name the folder appropriately (e.g., “Scripts”, “Reference Data”).
- Drag and drop nodes or embedded files into the folder.
You can also rearrange folders as needed, and even apply operations (e.g., show/hide) to multiple nodes grouped inside them.
Adding embedded files
To embed a file into your SAMSON document:
- Go to the appropriate folder in the Document view.
- Use the context menu to add files, or drag them directly into SAMSON.
All embedded files are stored inside the document, so once added, they travel with the file even if you email it or copy it to another device.
Practical example
Imagine running a series of simulations over a molecule. You can embed:
- Your raw structure files
- Preprocessing scripts (Python)
- The output data (CSV, TXT)
- A PDF you write with notes
Then zip the SAMSON document and share it with a collaborator – all in one package and no dependencies to worry about. That’s both efficiency and peace of mind.
Conclusion
Embedding files and folders within SAMSON documents solves a very real problem in computational molecular science: keeping work organized, reproducible, and portable. It’s a small feature with a big impact on how you manage your modeling projects.
To learn more, visit the original documentation page: https://documentation.samson-connect.net/users/latest/documents/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.