For a couple of years I've been studying the problem and analysed the sources of error. The faults are:

There is one more complication, but we can ignore it. It is too small for us to apprehend and we can't do anything to correct it anyway.

When the faults are analyzed, we see that they both cooperate and counteract. In the bridge the first two faults cooperate, but in the nut they counteract. If a fretboard has the right amount of reliese to compensate for the "clothesline effect", these faults can be perfectly corrected by compensations in both the nut and the bridge. The problem is to find the right balance between the nut compensations and the bridge compensations, for if the release point is moved in one end of the string the release point in the other end of the string will be affected. By measuring the faults, I can calculate a perfect balance between the compensation in the nut and the bridge! That's my business idea.

• Intonate your instrument perfectly to equal temperament. My method doesn't use so called "offsets" which are pure guesswork. Instead I measure the faults and calculate the corrct compensations. Sterner Compensation^TM will give you correct results with a standard tuner or by any method of tuning.
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• Most likely it is sufficient in most cases to intonate the instrument to equal temperament but if you play a lot together with pianos or work in studios, I can stretch the tuning to match the stretching of the middle range of the piano or the grand piano.

• In consultation with the customer desicions are taken about:
  -  truss rod adustment,
  -  adjusting the string height (action),
  -  grinding or replacement of worn frets,
  -  alternative solutions for the intonation (see below).
• Measuring the faults of the instrument.
• Calculation of the compensations in the bridge and nut.
• Then I do the practical intonation. Each string is given its correct release point in both the bridge and nut.
  -  To move the release points at the bridge without altering the string height, I use light curing composite, the same material as dentists use for mending teeth. In most cases this is sufficient but quite often the compensations are too large. Then I preferably make a wider saddle that fits in the original slot - so that I don't have to alter the instrument. If you want to keep the saddle thin, the bridge can be reslotted, but that will cost more and it is unlikely that the result will be better. This applies to acoustic instruments. Electric guitars are easier to adjust at the bridge.
  -  At the nut there are two alternatives: Either I cut the fretboard and move the original nut forward to the release point for the shortest string, or I can make a new nut extending the corresponding amount over the fretboard. The latter being the more expensive, but then I don't have to make any alterations to the instrument. Then I rout back the release points for the other strings to their correct positions.
• A vintage instrument can be intonated without alterations to the instrument. It can easily be restored to its original apperance - if it, for some odd reason, is desirable.
• If you want to alter the string dimensions or string heights on the instrument, (e.g. in the studio), I can make different sets of compensated saddles and nuts for different setups.

Once I intonated a guitar built by Swedish master luthier Michael Sandén. It had a zero fret and intonated rather well. At the zero fret the three heaviest strings were 0.5 cent false and the three treble strings were about 1.5 cent false. I didn't want to touch the zero fret, so I intonated the bridge only. However, this customer (Petter Hölaas, Intelligent Sound) was not satisfied. He is blind since early age and his hearing is extremely developed. I had to compensate the zero fret with composite under the three worst strings. Then he was satisfied.