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These are COOT_HOME, which hosts the .coot.py file and .coot-preferences directory, and COOT_BACKUP_DIR, where intermediate, backup pdb files are stored. For a multi-user Windows computer the Administrator might want to change these environment variables in the runwincoot.bat file (by default in C:/yourWinCoot) for every individual user (you obviously need a runwincoot.bat file for every user).