Some preferences can be saved between sessions using Fox. Those are saved in a file
$HOME/.FOX-Free Objects for Crystallography` under linux).
Note: the preferences are not created globally - i.e. the first time you launch Fox (or a version of Fox posterior to 2006/10/29), not all preferences will be available until you use the feature that requires it. e.g. to enable the default display of the asymmetric unit in the 3D crystal view, you must first have opened a 3D crystal view, which will create the preference. Only then will that option appear in the preferences dialog.
The following options can be modified:
Use compressed file format (``.xml.gz``)
Automatically open crystal 3D view when opening or creating a new crystal structure (if loading an xml or cif file, it will pop up the 3D view immediately).
Default: display only asymmetric unit cellin 3D view - you can change the display limits after the window is opened
Default: display atom names in 3D view
Default: use Dynamical Occupancy Correction
Automatically open powder pattern graph - this will be diasabled if there are no data points
Default: display reflection indices