Guess you mean the MySQL Control Center GUI. I have not checked the latest version recently but I do not think so. I tend to use MySQL Front which I can recommend for many things but only has a relatively crude tool for copying between MySQL databases - it basically does a create table then inserts rows one at a time so is slow.
I you want to copy large databases (which we do) the options I have found that you are left with are:
1. Physically copying the database/tables - fast and OK for a one off but you need to take the databases down and be careful of file ownership and permissions etc..
2. Backup and Restore using standard MySQL tools see the manual - some require that you take the database down - you could check out mysqlhotcopy
3. Simple Perl script that uses the MySQL DBI to connect to the two databases and copy from one and create on the other - has the advantage that it can copy just as easily between hosts etc.. and is relatively fast We wrote our own but I cannot believe someone else has not written one so you could try searching CPAN
Depends why & how often you want to copy between databases
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