The conversion part of the manual is online here:
http://www.calibre-ebook.com/user_ma...onversion.html
If it's a variety of formats then enabling preprocessing and tweaking the line unwrap factor there is what you need in general. IIRC mobi - which might be prc as well - is not subject to the line unwrapping preprocessing logic at this point in time. If it's actuall pdb or something else then unwrapping should work. If it doesn't work on the first try you could do something like convert to Lit and then convert the lit file with preprocessing enabled back to mobi.