Resetting permissions and ownership on all DA related system files.

If you've just transferred all of your data to a new disk:
eg: http://www.directadmin.com/paths.html

if the ownerships and permissions are not correct, then you can get the set_permissions.sh script to do it for you:

cd /usr/local/directadmin/scripts
./set_permissions.sh all

Note that this script will not touch files uploaded by your users to public_html/private_html folders as it doesn't know what their permissions should be.
If you are not worried about potential permission problems and just want a very basic level of operation for all of the files your user have uploaded (eg, if all of their files are owned by root and you need to change them), then you can run the following for a basic reset of the permissions (change domain.com to a real domain name):

./set_permissions.sh domaindir domain.com