I built my own guitar 8 months ago under instruction by a master craftsman. On the last day of construction we adjusted the intonation by filing off some of the leading edge of the saddle under the different strings. We took each string in turn and checked the intonation against an electronic tuning app before making adjustments. But guess what... when I got the guitar back home where the altitude is much higher than the coastal town where I made the guitar, the intonation changed. Also, as the strings settled in after dozens of tuning exercises the intonation changed again. I started making further changes to the saddle until now the bone edge looks ... well, wavy is the best word to describe it
So I started doing some research (something I should have done right at the start), and this is what I ascertained:
1. Intonation issues will be different for different tensions, and even makes, of strings.
2. The intonation will change a little as the new wood of the guitar settles in and ages.
3. Humidity levels will effect intonation.
4. The pressure and angle of the finger when fretting at the 12th will effect intonation.
5. Even the best made guitars will have some intonation issues (probably because of 1 to 3 above)
Then the GREAT REVELATION .... the human ear can only detect differences of more than 3 cents and sometimes even 5 cents... SO WHAT"S THE POINT OF FUSSING OVER AN INTONATION DIFFERENCE OF LESS THAN 3 CENTS!
To allow for differences in actual tuning of the open strings I took whatever the actual Hz reading was on the open string and doubled it to find what it should be at the 12th fret... then I fingered the string at the 12th and compared the Hz reading against what it should be. The results for my guitar yielded the following intonation differences:
Top E -0.5 cents
B -0.2 cents
G +1.3 cents
Bottom E 0.0
The notorious G string has the biggest problem but still way below my hearing threshold... so why mess around with the saddle.
I am a novice so very happy to be corrected if I have got it wrong