Loading molecules

You can load a molecule via Home menu > Open or via the Ctrl + O shortcut on Windows and Linux or Cmd⌘ + O on Mac. To open a recent file, follow File menu / Recent, where you will find a list of the recently opened files.

SAMSON will use an appropriate Importer to load the chosen file format. By default, SAMSON has importers for several file formats, e.g.: SAMSON formats (.sam, .samx), PDB format. If you want to have more importers, please, follow to SAMSON Connect to the Elements section and check for other importers (see SAMSON Connect Elements section for more information).

Depending on the importer and the file format you might need to specify additional parameters used by the importer. For example, the PDB importer needs you to specify the parameters 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 the viewport.

Molecules also can be downloaded with the help of specific Apps, like PDBDownloader, which allows one to download a pdb file from the RCSB Protein Data Bank. You can also donwload documents shared in SAMSON Connect - Assets.

Downloading a document from Assets


The loaded or created molecule is placed in an active Document. In one SAMSON instance you may simultaneously have several Documents opened, but only one Document is active at any given time - the one you see in the document view.

The document view

Having several Documents is useful when you want to do different not-connected tasks with different molecules.

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

To switch between Documents, open the Home menu and choose the desired Document in the Documents list, or use the Ctrl/ Cmd⌘ + Tab or Ctrl/ Cmd⌘ + Shift + Tab shortcuts.

Switching between documents

See document view and node types for more details.


A Document may have several folders which can be used to arrange any types of nodes together, to apply operations to sets of molecules, e.g. hide or show them in one click. To create a new folder, use the Ctrl + Shift + F shortcut on Windows and Linux or Cmd⌘ + Shift + F on Mac or click on Add folder... in the Edit menu.

Edit menu