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chrisryn:
Set your tools however you want. Then adjust G54 Z so that when G54 is active that Z=0 is the face of the chuck. From your description I believe this is your current method. Now if you want your working coordinate system to have Z=0 at 3" away from the chuck face, then insert the instruction
G52 Z 3.0
After this instruction and until changed your working coordinate system is changed by the content of the G52 registers.
In Fanuc at power on, program start, and various other changes of operating mode the G52 regsisters are all zeroed.
The G52 values are added to whatever the current active G5x is. However, you may need a sign reversal in the G52 Z command. Experiment to determine the sign to use in the G52 Z command, and do it with G54 set away from the face of the chuck.
You can put the offset value in the G52 command with a variable. Such as
G52 Z #500
Prior to the G52 you can insert a test on #500 that would prevent being closer than some desired value from the face of the chuck.
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