Hmmm. 
I usually do my own adjustments with my bass, and the following are stuff i
learned so far:

1) actual scale length
You may want to check up on the exact length that the neck is fretted for -
you can easily get that with some math and the fret lengths. if your fret
scale is not the same as the string length at the low "E", then you may have a
problem. For some reason, this doesn't always hold true - I chalk it up to
certain scale lengths being more forgiving than others.

2) string set
admittedly, the combination of player and instrument influences how intonation
is - some people have a light touch, some don't, and guitars (even in the same
manufacturer and type line) have very individual feels and "give" in terms of
resonation. If you're not getting good intonation, that's another thing to
look at: matching the string type to the player and the player's guitar.

3) frets
Sometimes, the frets themselves may be the problem; some may be raised because
of loose installation, or the fret may be slightly skewed.

4) neck
The neck itself may be slightly out of alignment, causing an intonation
problem. other problems with the neck include necessary readjustment of the
neck's bow curve, via the truss rod. At worst, the neck may have a twist.

5) bridge
bridge height and fine tuning is the easiest to solve, but it's also good to
look at how the bridge is anchored to the wood - while it may be solid with
the strings at playing tension, when loose, it may be wobbly. another thing to
look at is if the actual height of the bridge is matched to the string height
as it pertains to the guitar's actual construction.

Hope this helps!

On 09/03/06, Reynolds, Jason M. <[EMAIL PROTECTED]> wrote:
>> Since intonation is related to string length, I figured you might be
>> treading dangerous water with how short the distance is between the bridge
>> and the nut.  You might want to try a different gauge as that affects
>> intonation.
>That's interesting, the length of even non-speaking string still has an effect?
>Oddly enough the intonation is better at the 24th fret than it is at
>the 12th, and the other strings seem to be alright. This may be a
>career opportunity for me so I'm open to learn anything there is to
>learn about it.
>          John

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