One of the outstanding Master Appliantologists at Appliantology.org, Budget Appliance Repair (a.k.a., Willie) offered the following procedure for assessing the operational state of the magnetron:
Disconnect the two wires going to the magtube and set it for 20-30 seconds and run it. If no abnormal noises and no smell with magtube disconnected, (MAKE SURE BOTH WIRES THAT ARE DISCONNECTED FROM THE MAGTUBE ARE SAFELY AWAY FROM EVERYTHING AND MAKE SURE NOT TO GET NEAR THEM!!!!!!!), the most likely problem is a bad magtube.
If you short the capacitor, carefully with an insulated screwdriver after doing the above test and it sparks you can be pretty sure
the magtube is bad also.
If everything else checks OK and the smell is kind of a sweet plastic burning smell, (I don't know how else to explain it but once you've smell it once you will know for sure the next time), then it's for sure a bad magtube.
Source: Advantium 220 microwave electrical burning smell
And more from another post:
Do you also notice what seems to be a louder then normal buzzing/vibrating noise.
If so, take an amp reading and see how many amps the unit is drawing, (the one I worked on only came up to around 2.4 - 2.6 amps), and you could smell that burning magtube smell after a minute or so of running.
Then pull the two wires of the magtube and make sure the are away from everything and start it up again and see what the amp reading is, (I got around 5.6 amps and the heavy vibration noise wasn't there any more).
A good working microwave will draw about 2 - 3 amps when first started and in about 3 seconds, (after the filament is warmed up), you will see the amp draw come up the the full 11 - 12 amps that a microwave will pull. If you listen carefully when a magtube ramps up power, (you will here a real light buzz noise after the filament warms up), you will see how that corresponds to the amp raise.
Source: GE OTR Microwave JVM1871SH001