File formats/Converters

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File Formats

Converter software for coordinate file formats

How to convert your file from one format to another:

Using downloaded software

  • Open Babel
  • Balloon calculates 3D atomic coordinates from 1D or 2D information on connectivity. It can generate an ensemble of conformations. It may also assign partial charges to atoms. It runs in a command-line on Linux, Mac OS X or Microsoft Windows.
  • Reads either a SMILES, an File icon.gifsdf file or a File icon.gifmol2 file
  • Outputs 3D atomic coordinates in an File icon.gifsdf file or a File icon.gifmol2 file and atomic partial charges in the latter format.


  • E-BABEL Interactive Molecular Structure Formats Interconversion Program. Part of the Virtual Computational Chemistry Laboratory; uses the Open Babel engine.
    39 input formats, 48 output formats; by file upload; Java-based.
  • Molecular Formats Converter in the WebQC.Org Chemical Portal, by Vitalii Vanovschi.
    50 input formats, 57 output formats; allows to add or delete hydrogens; by file upload or by text entry. Returns result in a text box.
  • Online demonstration of the CONVERT program by Molecular Networks.
    34 output formats; by file upload.
  • Jmol 12 (application and signed applet) can load text strings in SMILES or JME formats and convert them to 3D models using external web servers.
    See File formats/Chemical Structure for details.
  • Convert SMILES1D, InChI1D or InChIKeys1D
    to InChI1D, JME2D, MOL3D, SDF3D, XYZ3D, PDB3D, MOL23D, GIF2D, PNG2D,... using the CACTUS server at NIH: