This is a guide to acquire the primal stone fragment from the machine in the Baron’s laboratory in the Northcrest Manor in Chapter 6 A Man Apart in Thief 2014.
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Activating the Machine
To acquire the primal stone fragment in the Baron’s Laboratory first go down the stairs and pull the lever:

Pull the Lever to Activate the Machine that Breaks the Glass so you can Acquire the Primal Stone Fragment in the Baron’s Laboratory in the Northcrest Manor in Chapter 6 A Man Apart in Thief 2014
Breaking the Glass
Go up the stairs and turn the left wheel so that the spinning parts of the machine start to vibrate. Turn the right wheel so that damage is done to the glass:

Use These Wheels to Break the Glass to Acquire the Primal Stone Fragment in The Baron’s Laboratory in the Northcrest Manor in Chapter 6 A Man Apart in Thief 2014
Once no more damage is being done change the left wheel to a new position where the spinning parts vibrate and then the right wheel to do damage.
Acquiring the Primal Stone Fragment
Keep using the wheels until the glass breaks and you can pick up the primal stone fragment.