The ChimeraX Settings dialog is listed in a standard platform-dependent location in the menu (for example, UCSF ChimeraX... Preferences on a Mac), and contains sections:
Save saves the current settings, Reset replaces the current settings with the initial (“factory”) defaults, and Restore restores values that were saved previously. The Buttons below... option indicates whether these buttons should apply only to the currently shown section or to all sections of the Preferences dialog.
Several other preferences do not appear in this dialog, but in separate, tool-specific interfaces.
ChimeraX preferences are stored as multiple files in a standard platform-dependent location (for example, under ~/Library/Application Support/ChimeraX/ on a Mac). The location can be reported with command:
info path user unversioned configPreferences files are named according to the modules to which they apply, and are not created until nondefault settings are saved.
Model number will be included when multiple models are present.
Some preferences do not appear in the main ChimeraX Settings dialog, but can be adjusted and saved by other means: