One of the most common challenges molecular modelers face is managing and sharing complex projects. From structural models and simulation data to custom Python scripts and supporting documents, research often stretches across numerous files and folders.
This becomes especially tricky when switching machines, collaborating with remote colleagues, or continuing work across institutions. Misplaced files, broken links, and inconsistent setups are more than inconveniences—they risk project reproducibility and valuable time.
Fortunately, SAMSON’s document system offers a practical solution: full **file and folder embedding**. Instead of referencing external files, you can embed everything directly into a single SAMSON document. It keeps your entire molecular project self-contained and portable.
What Can You Embed?
Almost anything. SAMSON documents support embedding:
- Structure files (like PDB, mol2, etc.) for molecules
- Python scripts used for automation or analysis
- Images, PDFs, reports
- Simulation data and external datasets
- Anything else — the system accepts generic files
When embedded, these become part of your SAMSON document. That document can then be saved, shared, or transferred—no need to zip external folders or send email attachments that get separated from models.
How It Works
To embed a file into your document:
- Go to Edit > Folder to create a new folder (if needed) to organize files.
- Add your files to this folder within SAMSON.
- They’re now embedded directly in the document.
Here’s where you can manage folders:
Transferring Documents Between Computers
Once your project is embedded into a document, you can:
- Transfer the file to a different machine without worrying about missing resources.
- Archive the document as a snapshot of your work.
- Share the entire project with a collaborator in a single file.
This is especially helpful in institutions with strict file-sharing policies, vpn-restricted storage, or when researchers change machines (e.g., from the lab to home workstation).
Why Use Embedded Files?
The main reasons:
- Reproducibility — ensures everything needed for a project is always together.
- Collaboration — simplifies sending and reviewing complex designs.
- Backup — store a full version of your molecular design session.
- Convenience — no longer worry about broken file paths or missing dependencies.
Want to Learn More?
Check the detailed documentation on project embedding and file handling at SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON and start organizing your molecular modeling projects more effectively at https://www.samson-connect.net.