Rebuild Spotlight index?

Is there any way to rebuild the spotlight database from scratch? Mine is missing a lot of files for some reason - they don't show up when I search unless I open them first; I think it's because I did a clean install of Leopard and then copied my old files over, because it's those files that don't show up. So can I rebuild the database? If not, what should I do?

Okay, I did that, then rebooted, and after Spotlight said it was done indexing the files still didn't show up. Any idea why that would be?

I found out a bit more about what the problem might be. As I said, I did an archive and install and then copied my files over. When I did this, some of the files couldn't be read so I had to change the permissions, and those files are the ones that don't show up. Does anyone know how to fix this? Any help is appreciated.