When working on complex molecular simulations or modeling projects, you often find yourself juggling several files: molecular structures, input data, analysis scripts, results, figures, and supporting documents. Managing this collection can become frustrating—especially when transferring the project between collaborators or devices.
In the SAMSON molecular design platform, there’s a built-in feature specifically designed to address this pain: Universal File Embedding. This feature allows you to embed any number of files and folders directly into a SAMSON document, keeping everything in one place.
Why Embed Files in Your SAMSON Documents?
- Stay organized: Keep scripts, notes, data, and visualizations together in context.
- Simplify sharing: One file contains it all. No more zipping folders or hunting for missing dependencies.
- Reproducibility: Embedded scripts and data ensure future you—or collaborators—can reproduce your results.
- Portability: Transferring between computers or sharing with others becomes seamless.
Steps to Embed Files and Folders
You can embed your data files and folders in SAMSON in two ways:
- Drag and drop files or folders into the SAMSON interface. A dialog will appear asking if you’d like to embed them.
- Or, use the top menu: Home > Embed files (for individual files) or Home > Embed folders (for full folders).
Once embedded, the files become part of the SAMSON document structure. That means the document file now carries everything you’ve added. There’s no need to maintain separate directories or manual logs of relevant files.
This is particularly useful when working with:
- Python scripts for simulation control or data analysis
- Jupyter notebooks with plots and documentation
- Datasets for machine learning or calibration
- Figure assets for publications
- Supplementary material such as PDFs or readme files
How to Access Embedded Files
After embedding, you can access these files through the document structure in the Document view. Embedded items are stored alongside your models and are maintained when you save or share the document.
Need to update an embedded file? You can re-embed the updated version, or store a version history by embedding multiple versions with different names.
Use Cases in Collaboration
If you’re collaborating with colleagues—especially across institutions or countries—Universal File Embedding ensures all shared documents contain needed files. Combined with SAMSON Connect, it becomes easy to publish a complete molecular project with embedded data, scripts, and visual results.
This way, collaborators don’t have to ask for auxiliary files or resolve mysterious errors due to missing dependencies. Everything travels together in a single, self-contained project.
A Simple Way to Stay Organized
Whether you’re preparing molecular models for analysis, running simulations, or compiling results for a paper, SAMSON’s Universal File Embedding is a useful tool that helps reduce clutter and increase consistency.
To learn more, visit the official documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.