Coming from a C++/Java background, going from the ground up in a new langauge can be a pain. This is espeically apparent when there are 1,000 opinions on the "proper" way to do something more complicated than the generic "hello world".
Personally, I found
An Introduction to PHP for Scientists and Engineers to be very helpful. It's a good way to make a website that takes input and displays data in an organized way. The book doesn't do database implementations at all. However, I also don't do databases (MySQL, Oracle, etc) for various reasons (either cost $ or take alot of time to make them less vulnerable), so I use proprietary hashed encryption for my important web data files with all of the associated performance and usability tradeoffs. I also don't do large-scale websites at all, so it works well for me. It's a short book, and Amazon/Google Books give a good enough preview that shows the general flow of the whole book. It's for beginners in PHP.
It's also good for scientific work because scientific data rarely comes in database form.
Good luck!