I’ve always checked my intonation using the 12th fret harmonic. But today I checked it with the fretted note and it’s a few cents flat.
That’s just weird. I am using the harmonic directly over the fret but when fretted it’s not the same pitch. I don’t get it. What’s going on? Some effect of the string bending?
I’m assuming I should use the fretted note for intonation and not the harmonic?
I think I know what you are talking about, @howard and I also think I have noticed it as well, but I want to wait until I get back to my basses in a few hours to see how they are faring or whether I can reproduce what you are experiencing.
One of my first thoughts, however, was: do you have a high action on that bass? Somehow I have a gut feeling (for whatever that’s worth) that it might be connected to action height…
Nope, medium low at the moment. Could be lower but not high at all.
Another theory: playing the harmonic, it’s the pure harmonic at the frequency you would expect. Playing the fretted note, there’s clearly more low end to the sound, and it’s picking up more of the actual tone of the instrument.
But that’s just a guess.
Yes, maybe…
I just checked briefly with my basses (and my tuner is probably not as good as yours), and ALL fretted notes at the 12th fret are sharp compared to the harmonics there. I had never noticed… but as you said, the harmonics are “purer”, while the fretted notes contains lots of other contributing frequencies.
It is almost OK for the Yamaha, but worse for the P-copy and the Fender Jazz (which I had never had for adjustment or done any myself).
Not sure if this helps any!? (Your fretted notes were flat - did I get that right)? One thing to remember is that at the 12th fret the string is only half as long as it used to be and perhaps slight variations in length become more pronounced!?
I have read others saying theirs was sharp too but mine is definitely flat.
If you normally check your intonation using the open string and the 12th fret harmonic… you aren’t really checking your intonation because you are taking fretting out of the equation.
Intonation is basically compensation for how much you pull a string sharp by pressing it down to the fret. To set (or check) intonation, one of the notes you are comparing needs to be fretted. Common methods include comparing open/12th fretted or 12th fret harmonic/12th fretted or open/5th fretted/7th fretted (splitting the error between the 5th and 7th).
Got it, that makes sense - so it’t the relationship between the fretted note and the harmonic, not just the harmonic, and I need to shorten that particular string a little.
Thanks!
That worked great, sounds much better now too. E string was pretty far out of intonation. Thanks again!
Awesome!
If you don’t mind (and have the time), @howard : could you write up a short how-to (or: how-I-did-it)for us hardware challenged bassers?! (I still have plans for doing my first setup/adjustment during the Christmas break) 
Thx!
As is obvious from the above I am not an intonation expert 
But it was really not too difficult, just a little time consuming. You might need a good tuner though.
Basically, what I did was repeat these steps. These will only work for basses with intonation screws on the back of the bridge for each saddle, which is common but not universal.
It turns out Marcelo has a video about this too, which I should have searched for before asking at all. He explains it all really well.
His other setup video is fantastic too, do it first before intonation:
Basically, to set up the bass, you want to do things in this order:
Thanks , Howard! That is what I call community service (I know it usually means something else, though…) 
Much appreciated!
So after putting new strings and adjusting the truss rod the E on my Fender P-bass the sound of my E string was still off. They did a really poor job setting this bass up since i could almost fit my finger in between the string and 12 fret. So I lowered the action as well. Marcelo’s instructions helped a ton.
I also noticed that on one of my other basses the intonation was off too. So my question is how often do you adjust this? Do you have to check it every time you put on new strings or when the strings are becoming “old”?
On a sidenote: the original Fender strings were really awful to play. I couldn’t play the bass for too long because it felt they were cutting in my fingers. Really weird and I didn’t had this problem with any on my other bass. The new La Bella (usually I have D’addario) strings that I used are fine, so I solved that problem but I was just wondering if anyone else had a similar experience.
Intonation I check every time I make a major change to setup but have generally found I only need to mess with it much when I change strings. I think this is very bass-dependent.
Yep, i’d suggest to never use harmonics for intonation and always use the open string and 12th fret. Some tuners may not pick up harmonics properly, the reason harmonics were used is that they’re easier to hear when tuning by ear. What i care about is what the instrument sounds like when i play it normally, not what the harmonics sound like. I have a Yamaha AES620 guitar that has big frets on it that i have to be extremely light with my touch or i bend the notes sharp!
Yeah. Open string and fretted is really all that matters. The fixation on the harmonic by a lot of people online confused me about this a couple years ago
It’s all really very straightforward and easy.
It really shouldn’t matter. If your tuner can pick up the 12th fret fretted then it should pick up the 12th fret harmonic because they are the same frequency.
As for needing a light touch on the guitar… you could make your vibrating string length a little shorter to suit your play style. After all, setting intonation is compensation for sting defection (stretching) when notes are fretted, so even if your normal finger pressure deflects the string all the way down to the fretboard you just have to compensate for it. But you have to be consistent with your finger pressure, i.e. not press down all the way to the fretboard sometimes and barely press down to the fret other times.
My harmonic is always the same as the 12th fret.
