If you’ve ever needed to transfer a molecular modeling project from one computer to another—perhaps to run simulations on a different machine, present your work, or simply share it with a colleague—you’ve probably encountered the hassle of handling multiple files and directories. Python scripts, input data, analysis outputs, supplementary notes… They all need to be kept in sync and correctly referenced. Unfortunately, scattered resources often lead to broken dependencies and lost information.
SAMSON, the integrative molecular design platform, offers a feature that many users overlook, but that could solve this entire issue: Universal File Embedding.
What is Universal File Embedding in SAMSON?
In SAMSON, your entire project—including molecules, simulations, models, and even Python scripts—can be stored into a single coherent entity known as a Document. Thanks to Universal File Embedding, this Document becomes a self-contained package that can include any number of files and folders. This lets you bundle configuration files, Jupyter notebooks, machine learning models, figures, even publications—whatever you might need!
How to Embed Files and Folders into SAMSON Documents
There are two ways to embed content inside a Document:
- Drag and drop files or folders directly into the SAMSON interface. A prompt will ask whether you’d like to embed them.
- Use the menu: Home > Embed files or Home > Embed folders.
Once embedded, the files are stored within the Document itself, which can be saved with complete internal references. This ensures integrity even when moved between systems, uploaded for sharing, or archived.
Why This Matters
Molecular modelers and computational scientists often work with interdependent tools. That small CSV file you forgot to copy? Or the Python script buried two folders deep? Broken links like these can prevent workflows from running correctly or reproducing previous results.
Universal File Embedding simplifies this. Now, a colleague can open your Document and have immediate access to everything needed—as it was when you last saved it. It’s especially helpful when:
- Collaborating with distributed teams.
- Archiving long-term research projects.
- Teaching—students can receive a pre-setup environment with learning resources embedded.
- Presenting at conferences or workshops, where connectivity might be limited.
Sharing Embedded Documents
Once you’ve embedded everything in a Document, you can publish it on SAMSON Connect. That way, others can interact with your full project—not just a static representation.
This makes your work portable, reliable, and easy to disseminate.
To learn more, visit the original documentation page: https://documentation.samson-connect.net/users/latest/loading-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net