MAC MAIL won’t open. asking about permissions
I've seen this once before and was able to fix it by deleting the index rather than changing the perms.  I didn't (and still don't) really understand what I did to get into the situation, nor what it did by deleting the files, but I got away with it.

Disclaimer: I use mac mail as an IMAP client so blowing away files willy-nilly isn't overly dangerous for me. If you delete each message from the mail server as you download it and the only copy of your mail is on your client, your mileage may vary, at the very least, take a copy of anything important.

On Mavericks, the indices are located in your home directory under Library/Mail/V2/MailData/Envelope Index