One common frustration when collaborating on molecular design projects is making sure all files stay together — simulation outputs, analysis scripts, papers, images, and custom data often need to be manually tracked and bundled when sharing or switching between machines. This not only increases the risk of data loss or confusion but slows down research workflows.
Fortunately, SAMSON, the integrative molecular design platform, offers a simple yet powerful way to solve this problem — by embedding files and folders directly into molecular documents via a feature called Universal File Embedding.
What Is Universal File Embedding?
In SAMSON, a document contains all the information about your molecules, structures, models, and simulations. But it can also do more. With Universal File Embedding, you can store any file or folder directly inside a SAMSON document — including Python scripts, entire apps, datasets, PDFs, notebooks, and more.
Once embedded, these attachments become part of your document. So when you share the document or transfer it to another machine, everything goes with it — no broken paths, no missing files.
How to Embed Files and Folders
There are two main ways to embed content into your SAMSON document:
- Drag-and-drop: Simply drag a file or folder into the SAMSON window. A prompt will ask if you’d like to embed it.
- Menu option: Use the commands
Home > Embed filesorHome > Embed folders.
The chosen files will be stored within the document itself. This means that even if you later delete the original file on your computer, it will still exist safely embedded in the SAMSON file.
Why This Matters
For molecular modelers working on research papers, computational notebooks, Python-based automation or ML pipelines, this embedding feature brings several benefits:
- Reproducibility: Keep scripts and data together with the molecule they analyze or simulate.
- Portability: Share research packages as a single file with collaborators or students.
- Presentation: Prepare self-contained molecular teaching files, complete with images, reference PDFs, and analysis scripts.
- Version control: Store draft data directly with your molecular model for easy retrieval.
You can always access the embedded content directly from the document view, enabling fast integration with the rest of your modeling workflow in SAMSON.
Final Thoughts
While tools for molecular modeling usually treat files as external dependencies, SAMSON’s approach makes it easier to focus on the science and reduce the project management overhead. Whether you’re building simulations, teaching molecular concepts, or analyzing structures with Python, Universal File Embedding helps you keep your work intact, reproducible, and easy to share.
To explore this feature further, visit the official documentation at 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.