Doctor Yellow is one of those elusive trains in Japan. It's used as a diagnostic vehicle, to check track alignment, alignment and quality of overhead electricity lines etc.
There IS a schedule, sort of, although most people will tell you that you can't fin out when Dr. Yellow is going to be in any particular place. In short, nothing runs without a schedule in Japan. Ask the right people, and you can find out when the good Doctor will be out of his shed.
One time you can guarantee that Dr. Yellow will be out and about is after a typhoon. This shot was taken after one of the recent typhoons passed through Tokyo. The reason the Doctor goes out after every typhoon is that there are, obviously more things to check and more reason to check them.
I did get lucky with this shot, though. I wasn't on my roof specifically to look for Doctor Yellow. I was there shooting the great sunset the day after a recent typhoon.
I was shooting the trains passing in the distance but, again, not especially looking for one train in particular.
I didnt even notice that I'd shot Dr. Yellow until I got downstairs into the house and realised that it was not a white train drenched in sunset colours I had on my camera, but a yellow train. It's not amazingly sharp as I was shooting at the very end of the light being good and the D800e is not great at 800 ISO. I was also shooting with my 300mm f/4 prime lens, hand-held and at 1/125th sec.