A molecular model rarely lives alone. Alongside the structure, a project may depend on scripts, images, input data, or research papers. When those files sit in separate folders, moving the work to another computer—or sharing it with a colleague—can turn into a search for missing pieces.
SAMSON documents can hold more than molecular models: they can also embed files and folders. That gives you a practical way to keep related project material together when you transfer or share a document. It does not replace good file organization, but it can reduce the number of separate items you need to track.
What a SAMSON document contains
The Document view shows the data graph of the active document. That graph can contain atoms, bonds, molecules, models, simulators, and other information. A document can also include files and folders, so a molecular structure and supporting materials can be stored together.
If you work on more than one system, SAMSON can have several documents open at once, although only one is active at a time. You can switch between them from the Documents list or through Home > Documents. Keeping separate projects in separate documents can make it easier to avoid mixing their contents.
Embed supporting files
To add files or folders to a document, either drag and drop them into SAMSON and respond to the prompt about embedding, or use Home > Embed files or Home > Embed folders.
Possible additions include Python scripts, research papers, images, datasets, and folders containing related materials. For example, if a model is accompanied by a script and a figure used to interpret it, embedding those items can keep them with the document rather than relying on someone to locate each file separately.
A simple handoff routine
- Open or create the document. Load a structure using Home > File > Open, or create a document with Home > File > New.
- Gather the relevant materials. Identify the files and folders that belong with this particular project. Include only what is useful for understanding or continuing the work.
- Embed them. Drag and drop the selected items into SAMSON, or choose the appropriate Embed files or Embed folders command.
- Share the document. Because embedded items are stored within the document, the document can be transferred between computers and shared.
This approach is especially useful when the structure alone does not tell the whole story. A paper may explain the scientific context; images may provide reference material; data or scripts may help a collaborator understand what accompanied the model. Keeping these materials together makes the handoff clearer and reduces dependence on a trail of separate attachments.
One useful habit is to decide what belongs in the document before sharing it. Embedding is a way to package related files, not a substitute for describing their purpose. A clear filename or folder structure can still help recipients understand what they have received.
For details 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.