You can save files in the following ways:
To save changes to the current file, choose GChemPaint displays the Save As dialog. Enter a name for the file in the Save As dialog, choose a file format, then click .-> or click on the toolbar. If the file does not have a filename,
To save a new file or to save an existing file under a new filename, choose Save As dialog box, choose a file format, then click .-> . Enter a name for the file in the
Available file formats are:
Native format (*.gchempaint)
Chemical Markup Language files (*.cml)
MDL MOL files (*.mol;*.mdl)
PDB files (*.pdb;*.ent)
XYZ Co-ordinate Animation Format (*.xyz)
Of course, only 2D data are exported, even if most formats support 3D coordinates.
The native format is supported directly by GChemPaint, Chemdraw formats and CML are supported through plugins, and other files are saved (and read) using the OpenBabel library http://openbabel.sourceforge.net.
Saving in a file format other than the native format is unsafe because not all features are supported either by the plugins or the OpenBabel library.
Other formats might be supported, depending on the OpenBabel version as explained in the section To Open a File.