For many molecular modelers, one of the recurring challenges is sharing complex research, simulations, or molecular systems with collaborators—especially when those projects contain many files, scripts, or associated data. Going back and forth over email or cloud storage, worrying about dependencies or missing files, or explaining how to run a model, can be frustrating and time-consuming.
What if you could bundle everything needed for your molecular modeling project—models, simulation results, Python scripts, images, and even documentation—into a single shareable file?
This is exactly what SAMSON allows through its shared documents system. In this post, we’ll walk through how to use shared documents in SAMSON to embed and publish complete molecular modeling projects, and why this can make your collaborative workflow easier and more organized.
Embedding More Than Molecules
SAMSON Documents don’t just store molecules. Thanks to the Universal File Embedding feature, you can embed entire folders, Python scripts, research papers, code, datasets, or any file needed for your project. This makes the document self-contained and portable across systems.
To embed files or folders:
- Drag-and-drop the files or folders directly into the SAMSON window, and choose to embed them when prompted.
- Alternatively, go to Home > Embed files or Home > Embed folders.
This is especially useful when developing or sharing machine learning apps, running simulations with custom inputs, or attaching analysis scripts and results.
Sharing Documents from SAMSON
Once your document is ready, SAMSON offers easy publishing options through SAMSON Connect. From the main interface, go to Home > Publish.
In the publish window, set the following:
- Name and description of the document.
- Visibility level:
- Public: Anyone can open it. Editing requires access rights.
- Hidden: Only accessible via a direct link.
- Restricted: Requires explicit permission for both viewing and editing.
After publishing, you’ll be provided with a direct link to share your document. This cuts down on lengthy explanations and ensures collaborators always get the latest and complete version of your project.
Receiving and Reusing Shared Documents
If someone shared a SAMSON Document with you, importing it is simple:
- Go to Home > Download in SAMSON.
- Browse online shared documents in SAMSON Connect – Documents.
After downloading, all embedded files, molecular data, and scripts will be available. No setup, no trying to chase down dependencies.
Good for Versioning, Great for Collaboration
With complex systems and team-based modeling, it’s easy to lose track of file versions. Shared SAMSON Documents offer a way to:
- Keep a clean, self-contained package for each version of your work.
- Reuse documents as templates across other projects or teams.
- Collaborate with students, researchers, or colleagues without worrying about what software or files they have installed.
Learn more about these features in the original SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.