This is a simple bash script I wrote to fix the permissions and ownership of files within a cpanel account. To use, simply copy the script your server, chmod 755, and pass the usernames as arguments:

./fixperms user1 user2 user3

You can also run a server-wide loop like this:

for i in `ls -A /var/cpanel/users` ; do ./fixperms $i ; done

Below is the script, but I recommend downloading it from here to ensure that the formatting is correct.

#!/bin/bash
# Script to fix permissions of accounts
# Written by: Vanessa Vasile 5/13/10
# http://thecpaneladmin.com

if [ "$#" -lt "1" ];then
echo "Must specify user"
exit;
fi

USER=$@

for user in $USER
do

HOMEDIR=$(egrep ^${user} /etc/passwd | cut -d: -f6)

if [ ! -f /var/cpanel/users/$user ]; then
echo "$user user file missing, likely an invalid user"

elif [ "$HOMEDIR" == "" ];then
echo "Couldn't determine home directory for $user"

else

echo "Setting ownership for user $user"

chown -R $user:$user $HOMEDIR
chmod 711 $HOMEDIR
chown $user:nobody $HOMEDIR/public_html $HOMEDIR/.htpasswds
chown $user:mail $HOMEDIR/etc $HOMEDIR/etc/*/shadow $HOMEDIR/etc/*/passwd

echo "Setting permissions for user $USER"

find $HOMEDIR -type f -exec chmod 644 {} \; -print
find $HOMEDIR -type d -exec chmod 755 {} \; -print
find $HOMEDIR -type d -name cgi-bin -exec chmod 755 {} \; -print
find $HOMEDIR -type f \( -name "*.pl" -o -name "*.perl" \) -exec chmod 755 {} \; -print
fi
done

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