| No - he's filing down the nut slots with a needle file - to get them lower - then he's checking intonation at the the 1st to 3rd frets. If your nut slots are cut too high, then it can mean that notes around the 1st to 3rd frets are sharp, as you have to press down too far.
Presumably, this was the problem Jaco had with the "cobbled together" bass that he used on the video - different body and neck, put together from a P and J bass!!
It also allows you to get a lower action overall, if you lower the height of the nut slots. Of course, if you lower them too far, then you will get a nasty buzzing, as the strings touch the fretboard "behind" where you are fretting the note - i.e. between fretting hand and nut!
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“Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that's creativity.”
Charles Mingus | 
