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Page 4 of: A Step-by-Step Guide to Acoustic Steel String Guitar Setup, by Thomas Becker   about me  

The Order of Things

Remember, to achieve that perfect guitar setup, you will have to make three adjustments: the neck relief (curvature of the neck), the saddle height, and the nut slot depths. If you do these things in the wrong order, then what you have already done will be messed up by the next thing you do, and you'll end up in some bizarre loop that will probably lead you into total frustration. However, if you make your three adjustments in this order:
  1. Neck Relief
  2. Saddle Height
  3. Nut Slot Depths
and you do Step 2 in manner that is slightly different from what many people will tell you (you will take the measurements for the saddle height with a capo on the first fret), then each of the three steps will leave the results of the previous step(s) completely unchanged. Hence, you'll get to your perfect setup in just three steps, with no backtracking necessary.
One More Thing: A Word about Alternate Tunings
If you ever play your guitar in alternate tunings, like open D, or DADGAD, then you know that in most alternate tunings, some or all of the strings are tuned down by a half note or whole note. This has two side effects:
  1. Since there is less tension on the strings, the neck does not get pulled forward as much as is the case in regular tuning. As a result, the action (distance between the strings and the frets) will come down a bit all the way along the neck.
  2. Those strings that have been tuned down will tend to swing out a little wider when you play them, again because there is less tension. That means they'll be more prone to buzzing.
Therefore, if you do your setup in regular tuning and then go down to an alternate tuning, you may find that you're getting the dreaded buzz. So if you ever use alternate tunings at all, you may want to do your setup work with the guitar in the "loosest" of your alternate tunings. Or, if you'd rather do the setup in regular tuning, you should aim for an action that is a little higher, like 5% higher, than what you would need if it weren't for the alternate tunings.