Story: I side-shimmed neck on my bass to get correct neck angle and better string alignment. Afterwards I adjusted the setup, especially focusing on intonation since tension and string length changed. During that I used "cable" tuner, not my everyday clip-on because a) it feels more accurate b) clip-on does not really feel vibrations when string is not opened. What I did: Started practice today, wanted to check if bass is in tune and if some changes to intonation are needed. Was too lazy with to get "cable" tuner, went for clip-on. Then, to get vibrations to the "head" side of string I plucked left of 12th fret, and got far-off readings. Then I realised that to get same (?) string length I need to fret on 12th fret from side of 13th fret. This got me readings pretty close to BEADG octave up, but actual BEADG. I checked, intonation in regular way is set, same tuner gives BEADG in usual way. I realize that saddles don't adjust string length from nut to 12th fret, so what I was getting in reverse is not adjusted; but how it then works as a whole? To make saddle adjustment even frest should move with it? Imagine fret positions painted on piece of rubber, and that piece of rubber is stretched - not only length is changed, all frets move a bit. Question: How bass may be "in tune" if I intonate only for open string and 12th fret, what magic makes other frets produce correct pitch? I suspect that both length and tesion are involved. Or I was lying to myself every time I did setup, and it is very improbable to get all notes correct.