A molecular structure rarely arrives alone. There may be a script beside it, a folder of input data, or a paper you need to consult while working. If those materials stay scattered across folders, it can be difficult to remember which files belong with which model—or to move the work to another computer without leaving something behind.
SAMSON documents offer a practical way to keep related material together: load or create your molecular content in a document, then embed the files and folders that support it. This is especially useful when preparing a project to transfer or share.
First, get the structure into SAMSON
Open a local structure using Home > File > Open. The keyboard shortcut is Ctrl+O on Windows and Linux, or Cmd+O on Mac. SAMSON chooses an importer based on the file format. Depending on the importer, you may be asked for additional parameters. These start with defaults; if you change them, the settings are saved for the next use of that importer.
If you need a structure from the RCSB Protein Data Bank, the Fetch Structures app is available from Home > Fetch. It can download PDB, mmCIF/PDBx, and MMTF files. For a local file, SAMSON’s available importers depend on the installed formats; additional importers can be found through the Marketplace on SAMSON Connect.
Once imported, the structure appears in the active document and in the viewport. The Document view shows the document’s data graph, which can include atoms, bonds, molecules, models, simulators, and other content.
Open a file or embed it?
Opening a file imports its contents into SAMSON. Embedding is useful for the other materials you want to keep with the document: scripts, folders, research papers, images, datasets, and other files. In other words, ask whether you want SAMSON to load the file’s contents as part of your working model, or whether you want to keep the file itself inside the document as supporting material.
To embed files or folders, drag and drop them into SAMSON and choose to embed them when prompted. Alternatively, use Home > Embed files or Home > Embed folders. The files and folders are stored within the document, making it self-contained and easier to transfer between computers or share.
A simple preparation routine
- Open the structure you want to work with, or fetch it from the Protein Data Bank.
- Check the Document view to confirm that the imported content is in the active document.
- Gather the materials that explain or support the work, such as a relevant script, input data, or reference file.
- Embed those files or folders using drag and drop or the Home menu commands.
- Review the document before sharing or transferring it, so you can confirm that the structure and intended supporting materials are together.
This approach also helps when you have several projects open. SAMSON can keep multiple documents open, although only one is active at a time. Switch documents from the Documents list or through Home > Documents; create a separate one with Home > File > New. Keeping different tasks in separate documents can make it clearer which supporting files belong with which molecular system.
For further details on opening structures, 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.