Guitar Setup Help Needed

You are intonating the string length... Intonation is more accurate when the distance from the note to the bridge is accurately measured to pitch. If you apply too much pressure, the string is bent which causes this to be inaccurate.
That’s why I intonate with the same force that I play at. When you intonate with the lightest touch possible, your intonation is most accurate if you only play with the lightest touch possible. Real-world playing throws off that intonation.


Since you don't fret the open string, it is not compensated for "how I play"... Because it is always "fretted" the same.
The open string is the basis of your intonation. And it is always compensated for how you play because, as you say, you always play it the same way.


Also, do you fret every note on the E string the same? If not, then I think your results are going to be inconsistent at best.
Your results will always be inconsistent at best, regardless of what intonation method you use, because varying fretting force changes the intonation with every note. I don’t care how well my guitar intonates when it’s lying there with no one playing it. I care about how well it intonates under actual playing conditions, because that’s the only time when anyone can hear the intonation.


However, I was just making recommendations based on my experience.
Me too. ;)
 
Evil, evil G string. I thought it was just me! It just always sounds a tiny bit flat, or a pinch sharp, even when the strobe says it's perfect. I never have figured out why, and if others have the same issue maybe it's just the way it is.
And it's not on just one guitar...
The problem with fixed-pitch instruments such as guitar is that intonation is always a compromise. The pitch of the G note in a perfectly-intonated G chord is a few cents different from the pitch of the G note in a perfectly-intonated A7 chord. For perfect intonation across all chords, you’d need to have thirty frets per octave, and that ain’t gonna happen. :)
 
The problem with fixed-pitch instruments such as guitar is that intonation is always a compromise. The pitch of the G note in a perfectly-intonated G chord is a few cents different from the pitch of the G note in a perfectly-intonated A7 chord. For perfect intonation across all chords, you’d need to have thirty frets per octave, and that ain’t gonna happen. :)
I get ya... but why does this phenomenon seem to be so prominent on the G string??
 
In some cases, flipping the problem saddle around may help with intonation.
This

There's more travel available in the direction that the 'straight' edge of the saddle faces. Quite common to see LP bridges with a flipped saddle or two. Perhaps the bridge posts are set in just slightly off optimal positions

I get ya... but why does this phenomenon seem to be so prominent on the G string??
Everything in (and outside of) a g string is quite prominent
 
I get ya... but why does this phenomenon seem to be so prominent on the G string??
Because the G and B strings are the only pair of strings that aren’t separated by a perfect 4th, and the G string features prominently in many common guitar chords.
 
Because the G and B strings are the only pair of strings that aren’t separated by a perfect 4th, and the G string features prominently in many common guitar chords.

I don't think this is a logical explanation. If the interval had an effect, why wouldn't the B string be noticed for the same reasons? Would an all-fourths tuning eliminate the issue?

I'd suspect it's more likely inharmonicity (natural or from pickup pull) or pitch variation from temperature changes or pulling the string toward bridge/nut (e.g. classical vibrato). Sliding around a bit can make the G go audibly flat. All these things tend to be most severe on the thickest plain string.
 
I don't think this is a logical explanation. If the interval had an effect, why wouldn't the B string be noticed for the same reasons? Would an all-fourths tuning eliminate the issue?

I'd suspect it's more likely inharmonicity (natural or from pickup pull) or pitch variation from temperature changes or pulling the string toward bridge/nut (e.g. classical vibrato). Sliding around a bit can make the G go audibly flat. All these things tend to be most severe on the thickest plain string.
I don't think inharmonicity varies much between solid strings, and the G-string issue occurs with or without temperature changes. The effects of string pull shoukd be minimal and uniform across the solid strings of the nut is cut correctly.
 
the G-string issue occurs with or without temperature changes.

I'm talking about temperature changes from touching the string and sliding. Tuning at room temperature then touching the string for 10-20 seconds can easily drop the pitch 6-8 cents. Slide around between a few notes and it might drop another 3-5 cents. Play some chords with open g for a bit and it rises ~10 back to where you tuned it.

I think we'd need more information to explain what someone else is noticing though. For example does the string just sound funny but read in tune, or are certain notes clearly off with a tuner?
 
Does neck tension not play into this at all?

I think what you mean is the neck “relief”. The relief is the curvature of the neck, and is adjusted by loosening or tightening the trussrod.

When I set my guitars up, I start by putting a new set of strings on, and giving them a good stretch. When I feel they are sufficiently settled, I check to make sure they are tuned to pitch, and then check the amount of relief in the neck. (There are several good YouTube videos from guitar manufacturers out there that demonstrate how to do this). I next adjust the trussrod to give adequate relief. Next up is the action. I have a relatively light touch, and like my strings as low as they can get without too much buzzing. I adjust the strings to the desired height that works for me, and then use a small machinists ruler to check that each of the strings are about the same height off of the top fret (for a consistent feel across the radious of the fretboard). Tune to pitch and check for buzzing (repeat as necessary). Finally, I check each string for intonation. I use the harmonic of the 12th fret and compare it to the fretted 12th fret. I use approximately the same amount of pressure when fretting as I would during normal play.

I check all of these things every time I change strings. You would be surprised how often the intonation needs adjusting, even when changing out the same gage and brand/model of strings.

Again, this is just my routine. As we all know, there are plenty of ways to skin a cat.

Keg
 
Use your neck pickup and turn the tone down to at least half. Removes a lot of harmonics and overtones the tuner picks up.
 
I've always found the bridge pickup works best for tuning. Not sure why...
That's fine, it usually doesn't matter that much for me. That said, I have found that when a particular string is being persnickety, moving to the neck pickup and turning down the tone control usually does the trick.
 
I get ya... but why does this phenomenon seem to be so prominent on the G string??
Because it's "thick" and not wounded.

If you look at a true temperament neck, you will see how behind the traditional guitar frets the tempered notes are.
 
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