There may be a reason why the chain is out of place so you should make a couple of checks first.
If you release the door from the opener using the release cord (see image below) you should be able to lift the door to half open by hand and the door should stay at that point if you release it. If not, there is a problem with the door. There could be a bind or drag in the door mechanism or the springs may be damaged or need adjusting. I would recommend a professional address any concerns with the springs as the force involved is high and there is a lot of potential for a serious injury.
If the door seems okay, there may be a problem with the trolley or the opener itself. The chain may also have come off due to too much play in the sprocket on the overhead opener. That is usually an indicator of wear in the worm gear/ sprocket drive assemblies.
If everything looks okay and the chain just jumped or came undone then your best bet is to reinstall it following the assembly instructions and detailed illustrations in the owner's manual. You can view the manual online at Manage My Home using the model number 139.53645SRT3 (which is just a newer version of the same model) and the instructions in the link below. You can also use the manual to see how the lift and opener assemblies work and fit together by checking the assembly and parts sections.
Once the chain is back on try running the opener with the door still disconnected. If the chain and trolley move all the way up and back then everything should be okay but you may find a need to fine-tune the travel limit settings once the door is reattached. Again, the manual can help you with that procedure.