I'm having an issue where the stepper motor gear on the Silent Desk Clock binds with the second hand gear. I've also noticed that the second hand gear moves back and forth. Any ideas on what is causing these and how to resolve?
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The motor is missing steps and jumping back 1/50 of a step. It is deliberately weak to avoid chopping off a finger in the exposed gears, but it looks like it is not powerful enough to turn the gears. It could either be too much friction or too little power.
Start by looking for obvious sources of friction. Unplug the power and rotate the motor manually. It should spin easily. Look for rough spots where the motor is skipping.
The motor circuit was designed to have just enough power with a 5v Arduino and a high resistance stepper motor. It might not have enough power with a 3.3v Arduino or a stepper motor that deviates too far from the expected resistance. Check those things as well.