Saving a Molecule File

It is possible to save a molecule in any of the supported file formats. For more information about file formats, see File Formats.

In the case of a single structure, the default behavior of the save action is to save the molecule to the same file which it was opened from, in the same format. If you want to change the file name or format, click Save As.

If you are working with a new molecule, Save works the same way as Save As.

If you are working with a multi-structure file, both Save and Save As opens a dialog window where the parameters for saving must be defined.

On the Save and Save as dialogs, a Saving method tab can be opened by checking the Advanced checkbox. The first half of the tab offers the following choices:

  • All structures TOGETHER: Saves all structures together in a single file. This is the default behavior of saving. If you do not open the Saving method tab, this option is applied.

  • All structures SEPARATELY: Saves all structures separately into a single file.

  • Into SEPARATE FILES: Saves each structure into a separate file. In this last option, the numbering of molecule files begins with the molecule in the upper left corner.

The second option remains inactive unless the chosen file type supports multi molecule files (for example, MRV or SDF files). Similarly, for one molecule only files, only the first option is enabled.

The same applies to reactions and structures containing R-group definitions. Tn these cases, only the All structures TOGETHER option is available.

When the given parameters for saving (filename, format, and route) are the same as for an already existing file, the outcome is determined by the other two radio buttons of the dialog window. These are as follows:

  • Overwrite file: Replaces the original content of the file.

  • Append to end of file: Adds the new structures to the original file, so its content is preserved.