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Opening and saving molecules

Daedalus supports the following file formats:

  • Proteins: mmCIF (aka PDBx)
  • Small molecules: SDF, Mol2, GRO, XYZ, and PDBQT
  • Electron density: 2fo-fc mmCIF, Map, and MTZ
  • Force field parameters: dat, lib, frcmod, prmtop (Amber), and top (GROMACS)

There are several ways open a file: Click the Open button in the GUI, and select which molecule to open, filtered by extension. You can drag a file from your operating system's GUI into the application window.

File open dialog

You can also use the Recent button to show a list of recently-opened files Recent files dialog

You can also associate file extensions with Daedalus using your operating system's settings, so double-clicking a file in its GUI, etc will open it. Daedalus does not set up file associations on its own; this is up to you.

You can also open files directly from online databases by dating a molecule's identifier, or common name in the Query DBs field, then pressing enter, or clicking one of the database buttons that appears. See the Databases section of this documentation for details.