Keeping all your data organized and portable is one of the recurring challenges in molecular modeling. Whether you’re working on protein-ligand simulations, sharing results with collaborators, or archiving your work for future reference, one thing is certain: jumping between multiple files, scripts, and folders often leads to errors, missing dependencies, or broken workflows.
SAMSON, the integrative platform for molecular design, provides a useful solution to this problem with a feature called Universal File Embedding. If you haven’t tried it yet, this might become one of your favorite organization tricks.
Why embedding matters
When you’re working on a molecular modeling project, you often use not only structure files (like PDB files), but also analysis scripts, parameter files, documentation, images, and more. These files often live in different folders. If you’re sharing your project or moving it to another machine, it’s easy to forget something.
Embedding files and folders directly into your SAMSON Document means everything related to your project is stored together in a single, portable unit. Once embedded, the files stay within the document, and you don’t have to worry about paths, external references, or missing files anymore.
How to embed files and folders
There are two ways to embed files and folders:
- Drag and drop: Simply drag files or folders into the SAMSON window. A dialog will appear asking whether you want to embed them.
- Use the menu: Navigate to
Home > Embed filesorHome > Embed foldersto choose what you want to embed.
Once embedded, the files remain part of the document and move with it. So if you send the document to a collaborator – or use it on another computer – the entire context is preserved.
What can you embed?
It goes beyond structure files. For example, you can embed:
- Python scripts
- Jupyter notebooks
- Custom applications
- Machine learning models
- Simulation result files
- Images and diagrams
- Documentation or readme files
There are no explicit limits to what you can add. This is particularly useful for reproducibility and collaboration. If you like working with custom Python scripts for data analysis or molecular dynamics preprocessing, embedding them means they are always bundled with the corresponding molecular model.
Making collaboration and sharing easier
Another benefit of embedding is that it works seamlessly with SAMSON Connect. When you publish a SAMSON Document that has embedded files, all those dependencies are included. This reduces friction when sharing with collaborators – they won’t come asking for “that missing script” or “a file that won’t open.”
Keep your molecular modeling reproducible
Working on a publication? Want to make your project easily reusable in six months? Embedding makes your workflow self-contained. It helps you preserve the exact state of your work, something that’s often difficult when juggling external folders.
To learn more about file embedding – and the broader possibilities offered by SAMSON documents – check out the full documentation page: https://documentation.samson-connect.net/users/latest/loading-molecules/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.