Hi Lil =)
When working with rodents, the first thing you have to remember is that grabbing is not the way to go, because for them, it is eerily reminiscent of having an eagle, snake, or fox grab them. Being picked up and held is an aquired taste for most rodents; it requires very slow, patient steps, but the ends result is def. worth it!
I would suggest putting some serious one on one time into the rat, not in the form of holding, but in the form of stroking, hand-feeding, and simply letting the animal become aquainted with your hands. Hands are a scary thing for most animals; until they know that hands are positive things, they tend to think of them as just another dangerous thing coming to get them.
Once your animal is more comfortable with your hands, practice gently scooping the rat into your hands, and holding her just an inch or two over the bottom of the cage. She will be able to leave at any time, and that is the point; she needs to learn hands are not about control and confinment, but rather someplace she can choose to come at her own free will. As she gradually spends more and more time on your hands, try lifting her out of the aquarium and holding her. Praise her gently and calmly with stroking and a soft voice, and give her treats so she associates handling with positive things. If she gets uncomfortable and wants to run away, put her back so she isn't being held against her will, something that can be very scary for rodents as it sparks up instincts of being attacked by predators.
Over time, she should start warming up to the idea of being held. It will take a good deal of time and patience, but will leave you with a friendly companion. Good luck!