When working on complex molecular modeling projects, it’s not uncommon to have dozens of associated files: scripts, simulation results, plots, PDFs, datasets and perhaps even documentation. These extra files can quickly become difficult to manage, especially when transferring projects between computers, collaborators, or backup locations.
This is where SAMSON’s Universal File Embedding feature helps.
Why Embed Files?
Embedding files makes your project truly self-contained. Instead of maintaining a separate folder structure that has to be zipped, synced or shared alongside your molecular models, SAMSON allows you to bundle all related content inside a single document. Whether it’s a Python script for a custom simulation, a data file with molecular information, or a machine learning model, it can all be embedded directly.
How to Embed Files and Folders
There are two convenient ways to embed files or folders into your Document in SAMSON:
- Drag and Drop: Simply drag any file or folder into the SAMSON application window. A dialog will prompt you to embed it into your open document.
- Using the Menu: Go to
Home > Embed filesorHome > Embed foldersto embed items manually.
Benefits of Embedded Files
Embedding offers more than just convenience:
- Project integrity: all external dependencies and supporting files are stored safely within the document itself.
- Easy sharing: documents are portable and can be sent to collaborators or transferred between computers without worrying about missing files.
- Reproducibility: future you – or your colleagues – can reopen a SAMSON document and access the exact environment used for previous modeling and analysis work.
What Can You Embed?
Embedding is not limited to input files. SAMSON supports the inclusion of:
- Python scripts or full Python apps (for simulations or analysis)
- Data files in various formats (e.g., CSV, JSON, TXT)
- Visual content like images or plots
- Research publications or supporting PDFs for direct reference
Best Practices
Here are a few tips to make the most of this feature:
- Embed final versions of your supporting files, not transient or temporary files.
- Use meaningful filenames to keep track of your content.
- If versioning is important, consider embedding multiple versions or using structured folders.
When used effectively, embedding files can greatly simplify project organization and ensure that your molecular modeling work is consistent and shareable.
To learn more about embedding and managing your molecular documents, visit the full documentation page 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.