## Saving Your Work

The software provides a number of options available for saving your work. These are detailed in the following sections.

### Saving Everything

The most comprehensive approach for saving your work is available by selecting the `File->Save` or `File->Save As` menu options. These will save a P3D file with full details about the reference molecule, pharmacophore (including your changes, if any), and the contents of your Molecule Evaluation page.

### Exporting All Molecules

This command, accessible via the `File->Export->All Evaluated Molecules` menu option, allows you to save an SD file containing all of the molecules currently on the Molecule Evaluation page.

The molecules will be saved without information about 3D structure or any mappings to the pharmacophore. A single copy of each molecule will be saved, even if each has multiple mappings.

### Exporting Alignments

This command, accessible via the `File->Export->Checked Alignments` menu option, allows you to save an SD file containing the aligned 3D structures that are checked on the Molecule Evaluation page.

If multiple alignments are selected for an individual molecule, they will all be exported by this command.