One common frustration among molecular modelers is managing all the files that come with a single project: molecular structures, datasets, reference PDFs, scripts, and more. Moving your project to another computer or sharing it with collaborators can quickly become messy when you need to bundle several loose files together manually.
What if everything could just be in one place—structures, images, scripts, references—without needing to reconstruct the project every time you switch machines or send it to someone else?
This is possible in SAMSON, thanks to its support for embedding files and folders directly into a molecular document. This feature allows you to create a truly self-contained project—an especially useful capability when working across devices or in collaborative settings.
Why Embedded Content Matters
In SAMSON, a document stores the hierarchy of nodes—including atoms, molecules, groups, as well as scripts, paths, and other resources. But beyond modeling data, documents can also embed any types of files, from experimental datasets to explanatory PDFs or Python scripts used for automation.
Everything embedded into a SAMSON document becomes part of the document itself—no more broken links or missing references when transferring files.
What You Can Embed
- Images and reference diagrams
- PDF documents
- Log or result files
- SAMSON scripts (e.g., Python)
- Any other data essential to your modeling task
Folders can also be created within the SAMSON document. These work like standard folders, and you can group nodes or files in them. Whether you’re organizing multiple conformations of a compound, different simulation snapshots, or sets of scripts—folders help structure your workspace logically.
Creating Folders and Adding Files
To create a new folder inside your SAMSON document:
Edit > Folder
This will allow you to start grouping nodes or embedding documents into a cohesive structure. Once you have a folder, you can embed files directly into it or elsewhere in the document.
Once embedded, files and folders are stored within the SAMSON document. Since the file is self-contained, you can:
- Move it between computers seamlessly
- Share your entire modeling project with collaborators without breaking anything
- Ensure that crucial data and scripts are always available alongside the molecular structures
Practical Scenarios
Here are just a few ways this feature makes work easier:
- Educational use: Embed tutorial instructions directly within a SAMSON document so students always have context.
- Validation: Keep raw data and notes inside the same project as the molecular models during peer review or publication.
- Reproducibility: Store simulation scripts together with structures and parameter files.
This approach streamlines project management and ensures long-term usability. You can reopen the project months later and still find every relevant file in place—no searching through folders or resyncing cloud drives.
Learn more in the full documentation: https://documentation.samson-connect.net/users/latest/documents/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.