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I'd like to be able to do this as well.
I've just migrated a whole bunch of access dbs onto mysql only to find that I now have to re-index all of them by hand. erk.
I've come to the conclusion that it is not possible to do that with MySQL control center. I think maybe because it's not possible with MyISAM tables they haven't implemented it in the cc. I think you'll have to get cracking on code......