Hi, actually we started looking into that a while ago, one of the problem is that saving all the information (settings + mesh data) to one single file may result in huge file sizes, it's a problem to deal with versions and it's not easy to extend; so we are thinking of saving the entire workspace to a user specified directory with: - one file per molecule containing molecule structure information - one file per surface containing surface geometry and rendering properties - one file per molecule containing per-molecule settings (animation mode, rendering properties etc.) - one workspace.molekel file containing a list of all the surfaces/molecules/settings files Molecules will be saved in one of the standard molecular file formats (probably just a copy of the original file). Meshes will be saved in a standard format like OBJ or other standard. Since however this change is going to take some time we decided to postpone it until after the release of Molekel 5.2.