One of the frequent challenges molecular modelers face is sharing and reproducing complex projects across different machines or teams. If your simulation or model depends not only on molecular structures but also on associated images, scripts, or data files, transferring everything correctly can be a frustrating process. Files get lost, paths break, and reproducing a project becomes time-consuming.
In SAMSON, embedded files and folders offer a straightforward solution to this problem. By embedding files directly into your document, you can ensure that everything needed for your project is self-contained. Whether it’s an analysis script, a reference PDF, or an image output, all resources can travel with the document itself.
Why Embed Files?
Embedding files into a document makes the document portable. You don’t have to worry about recreating a file structure or sharing multiple items manually. This is particularly useful when:
- You want to send a project to a collaborator.
- You’re moving between computers or workstations.
- You need to archive your work for future reference, knowing it’ll stay intact.
Types of Files You Can Embed
There’s no restriction on the type of files you can embed. Some examples include:
- Images (.png, .jpg)
- PDFs (e.g., publications or notes)
- Scripts (Python, custom formats)
- Data files (CSV, JSON, XML, etc.)
- Structure files (PDB, MOL, etc.)
This flexibility allows you to customize your document as a central hub containing not only your models but also all supporting information and resources.
How to Embed a File
To embed a file into your SAMSON document:
- Open your document in SAMSON.
- Create a folder via Edit > Folder to organize your attachments (optional but helpful).
- Drag and drop the file into the SAMSON interface, or use a dedicated menu if available.
The file becomes part of the document and can be accessed through the Document view. Since it’s embedded, it will be saved as part of the .sam file.
Important: If you’re distributing your project or uploading it to a shared resource, no need to zip external files. Everything is bundled in a single document file.
What About Folders?
You can also embed entire folders. This can be particularly helpful if you’re grouping files by type (e.g., one folder for raw data, one for processed results). To create a folder, go to Edit > Folder.
Here’s an image showing the Folder creation step:
Simple, Self-Contained, and Reproducible
By embedding files and folders directly into your molecular modeling project, you simplify your workflows and reduce the chance of broken paths or missing data. It’s a small habit that can make sharing and archiving significantly more reliable.
To learn more, visit the official SAMSON documentation page on documents.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.