A molecular structure rarely travels alone. The modeler may also need a script, a paper, an image, or a folder of supporting data to make sense of the work. When these materials are scattered across a computer, moving a project to another machine can turn into a search for missing files.
SAMSON documents offer one way to keep related materials together: they can contain molecular models as well as embedded files and folders. That makes document organization worth considering before you share or transfer a project.
Think beyond the molecule
When you open a structure, SAMSON imports it into the active document. The document is the data container shown in the Document view; it can hold information about atoms, bonds, molecules, models, simulators, and more. You can also add supporting files to that same document using Universal File Embedding.
This is useful when a structure is only one part of the material someone needs to understand or continue your work. For example, a document can include the molecular model alongside a relevant research paper, image, dataset, or Python script. Python apps and folders can also be embedded.
Embed files or folders
There are two straightforward ways to add files and folders:
- Drag and drop them into SAMSON. When prompted, choose whether to embed them.
- Use Home > Embed files or Home > Embed folders.
Once embedded, the files and folders are stored within the document. The document can therefore be self-contained, which is helpful when transferring it between computers or sharing it with someone else.
A practical way to organize a shareable document
- Open or create the document you want to work in. To open a local structure, use Home > File > Open or the platform’s open-file shortcut. SAMSON selects an appropriate importer based on the file format; some importers may present parameters before loading.
- Check the active document. Loaded or created molecules and files are added to the active document. The Document view shows its data graph, so it is a useful place to confirm which document you are working in.
- Add the supporting materials that belong with the project. Embed relevant files or folders using the drag-and-drop prompt or the Home menu. Consider what another person would need alongside the structure, rather than adding unrelated material.
- Keep separate tasks in separate documents when useful. SAMSON can have several documents open, but only one is active at a time. You can switch documents from the Documents list or through Home > Documents.
Embedding does not replace good organization: choose clear, relevant files, and make sure you are adding them to the intended active document. But it can reduce the number of loose pieces that need to be tracked separately when you move or share your work.
For instructions on opening structures, managing documents, and embedding files, see the SAMSON documentation on loading molecules.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.