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Loading molecules

To load a molecule use Home > File > Open or the Ctrl+O shortcut (O as in Open) on Windows and Linux or Cmd+O on Mac. To open a recent file, follow Home > File > Recent, where you will find a list of the recently opened files.

SAMSON will use an appropriate importer to load a file based on its format. By default, SAMSON has importers and exporters for multiple file formats (see the list of supported formats). If you want to have more importers, follow to SAMSON Connect to the Marketplace section and check for other importers (see SAMSON Connect - Extensions section for more information on how to add extensions).

Depending on the importer and the file format you might need to specify additional parameters used by the importer as, for example, shown on the image below. The first time you use an importer its parameters are set by default, ones you modify them they will be saved for the next use.

PDB Importer dialog windows

Press OK or Enter and the file will be imported into SAMSON. You will see it in the Document view and in the viewport.

Molecular structures can also be downloaded with the help of specific Apps, like Fetch PDB (Home > File > Fetch), which allows you to download files (in PDB, mmCIF/PDBx, MMTF formats) from the RCSB Protein Data Bank.


Loaded or created molecules, files, and folders are added in the active document. You can see the document in the the Document view which you can open the Document view by clicking on Interface > Document view or via shortcut Ctrl+1 on Windows and Linux or Cmd+1 on Mac.

The document view

The Document view shows the data graph of the active document. Documents store all information about atoms, bonds, molecules, models, simulators, etc.

You can simultaneously have several Documents opened in SAMSON, however, only one document is active at any given time - the one you see in the Document view. Having several Documents is useful, for example, when you want to do different tasks with different molecules or copy structures from one document to another. To switch between Documents, click on the Documents list in the top-left corner of the menu, or Home > Documents, or use Ctrl/Cmd + Tab or Ctrl/Cmd + Shift+Tab shortcuts. You can also see there the number of opened documents.

Switching between documents

To create a new document, follow Home > File > New or use the Ctrl+N shortcut on Windows and Linux or Cmd+N on Mac.

To open recently opened documents, use Home > File > Recent.

See Document view, document, and node types for more details.

Embedding files and folders#

SAMSON Documents can contain not only molecular models, they enable Universal File Embedding and can embed Python scripts and any number of files and folders. This makes it possible to embed Python scripts and whole Python apps (e.g., machine learning apps), research papers, images, data, and so much more.

Embed file

To embed files and folders within a document, drag-and-drop them in SAMSON and you will be asked whether your would like to embed them or use Home > Embed files or Home > Embed folders.

Folders and files are stored within the document, making the document self-contained, so you can transfer documents between computers and share documents.

Shared documents#

SAMSON Connect provides the possibility to share Documents - see SAMSON Connect - Documents. You can also govern who can access your shared documents either when publishing them or in your account on SAMSON Connect.

Downloading shared documents#

You can download Documents shared in SAMSON Connect - Documents by clicking Home > Download.

Download a shared document from SAMSON Connect

Downloading a document from SAMSON Connect

Publishing documents#

You can also share your document by clicking Home > Publish.

Publish a document at SAMSON Connect

In the dialog window, fill in the name of the document and its description.

Publishing a document at SAMSON Connect

Then click Publish document and the document will be shared in SAMSON Connect - Documents and the link to it will be provided in the same window. You can access and manage all your shared documents in your account at SAMSON Connect.