If complex substructures are repeatedly used, it is useful to save them as custom fragments for future access. Once the desired structure is built or loaded, go to the "Save custom fragment" menu item in the Builder menu. First, pick the structure you wish to save, then define attachment points. The latter must be hydrogen atoms and will be later cycled through in the order the are specified in this dialog. Note: to specify attachment points, simply click them and they will be automatically recorded, while the focus point will be moved to the next field. You may enter up to five attachment points, and at least one.

Fragment name should be unique, i.e. it should not duplicate name of any loaded structure or another saved fragment. Once done, click ok, and a new button will be added in "Custom" panel of the fragment library.