Setting up the Jaguar. Slotting the nut, intonation and string adjustments.

I’ve already done enough work in levelling the neck and adjusting the alignment at the neck pocket to bring the guitar to a reasonably playable state. But as with all guitars – it takes a proper setup to get the best results. Of course, every player prefers a particular, familiar feel in the way their guitars are setup. It’s all a matter of playing style – but it’s not just a matter of forcing every guitar into a pre-determined set of parameters. Every guitar is slightly different. Every bit of the guitar geometry can differ slightly – resulting in a need to adjust each guitar individually – to best exploit it’s own geometry and characteristics.

Fender’s methodology – in creating a range of instruments built from pre-manufactured, standard pieces – slightly mirrors the approach of Henry Ford to car manufacture. In fact the Fender range of instruments is a common standard model, and a strating point for a lot of DIY builders and customisers. But there’s no getting away from the individuality of self-build projects – even if they may be closely based on Fender designs. Necks and bodies from different manufacturers come with different tolerances. Add to that the tendency for different models to play differently, and there’s a whole lot of possibilities. (The Jaguar, with it’s shorter scale length is reknowned for being a little “slinkier” in it’s feel, over that, say, of a Stratocaster or Telecaster).

It certainly helps, therefore, to have a few standard Fender specifications, to begin help establish target setup dimensions and tolerances. In setting up the Jaguar, it will also help to have a note of the basic measurements and perameters I’ll be working to. As usual, information for Fenders tends to come in a mixture of Imperial and in Metric units. US specifications normally come with measurements in thousandths of an inch. UK tolerances work in millimeters. Somewhat confusingly, tools are readily available here in the UK in both imperial and metric. This US/UK/Euro unit thing has been going on my entire life, and I’m well used to jumping from one to the other. It’s important to know which toools work in what measurement, and to know at all times which standard you’re working in. There was a spacecraft a few years ago, which was lost in the Martian atmosphere – all a mix-up, we were told, between Imperial and Metric measurements. You see what happens?…


A proper guitar setup should usually follow the same, basic sequence. Adjustments at each stage can, and do, influence measurements elsewhere – so only by following the proper sequence can you best approach the task. The sequence I always try to adopt, is as follows:

  1. Rough tuning
  2. Neck relief check and adjustment
  3. String height check and adjustment
  4. Pickup height check and adjustment
  5. Nut slot cutting to provide correct string clearance (assumes nut is in place and already pre-slotted)
  6. Fine tuning
  7. Intonation check and adjustment
  8. Final tuning and check

I find I can, sometimes, run through the sequence a couple of times before I eventually dial in the exact settings – but doing it in this order helps get the vital nut slotting dimensions right. Since it’s all too easy to mess the nut slotting up – it makes sense.

Rough tuning

The guitar is already strung, and is in rough tune – but it’s apparent that the intonation is well out. The guitar doesn’t tune over the six strings on the lower frets – which also indicates that the nut is cut too high. I lock off the tremolo with the lock switch to help stabilise the tuning process to work on the tuning. It also helps to standardise the placement of the bridge – since it’s able to rock with the tremolo action, and slightly shorten and lengthen the strings. I find it best to sit the bridge at the centrepoint of it’s forward and backward travel, and to make all subsequent adjustments with the bridge in this position.

Neck relief check and adjustment

Fender necks normally seem to have a neck relief of about 0.010″ (0.25mm). Although many players have setups which incorporate much less. This relief, also referred to as “neck bow,” helps the strings rise over the higher frets when fretted low down. There needs to be a little room for the string to vibrate – although too much can result in a very high guitar action, making play difficult. The measurement is taken by fitting a capo at the first fret and then, with a string fretted with one hand at the top (high) fret, by testing the gap between the bottom of the string and the top of one of the frets in-between the two fretted points, (usually around the 8th fret).

It’s at this point that I realise that my shimming of the neck has, quite radically, changed the geometry of the guitar. Of course, the shim was used to help improve the playability of the guitar, and it’s been highly successful to that end. However, it also seems to have raised the heel of the neck in relation to the nut and bridge. Sighting along the neck shows the neck is pretty flat under string tension – but the neck angle alone is sufficient to keep the strings clear of the frets, and there’s no need for any neck bow. I check the neck relief with a .010″ feeler gauge, and I’m suprised to find the clearance is much lower. When I try with thinner gauges, I’m amazed to find the clearance a little under 0.004″. I’m not complaining. The action – even with the nut cut way too high – still feels good, and my fret levelling seems to allow a nice, low action all round. I might have to come back to revisit the neck relief – but the signs are good for an ultra-low action.

String height check and adjustment

The Staytrem bridge is a wonderful piece of kit. Instead of the individual saddle height adjusters you sometimes find on Stratocasters and Telecasters, the saddles on the Staytrem are pre-adjusted, and remain in the same, relative height on the bridge piece. The whole bridge however, is adjustable in height at the treble and bass side by two hex screws which sit and pivot inside the two ferrules or “thimbles” that are inserted into the body. Raising or lowering the string height, or action, is just a matter of adjusting these two screws to provide the best action possible for the player. The best part about the pre-set saddle placement is that there is no subsequent need to adjust the saddles to follow the curve of the 7.5″ radiused fingerboard. That adjustment is already pre-set.

The action is normally measured, for adjusment, at the 17th fret. I use a special gauge (designed by Chris Alsop Guitars), which allows for very fine and accurate measurement. However, after that, I always check each string manually at each fret, to see if any fine adjustment is possible, or desired. Fender recommend string heights of 0.0625″ (1.6mm) for the high “E” string, and 0.078″ (2.00mm) for the low “E” string. By adjusting the bridge and by checking playability to suit my style, I manage to settle the action at 1.4mm on the high “E”, and 1.6mm on the low “E”. That looks to give me a little leeway if it all settles down and I end up with a little buzz up the neck. But for now – that’s nice and low – just the way I like it.

Pickup height check and adjustment

The height of the pickups under the strings dictates some of the sonic character of the guitar. Too far away, and the pickups can sound dull, or under-powered. Closer pickups are louder, but harsher. Too close, and the magnetic poles can interfere with, or choke, string vibration. Closer pickups produce more output, but too close, and you’ll discover why the sound of trebly, single coil pickups is sometimes referred to as, “the ice-pick”. The measurement, for adjustment, is taken between the bottom of the strings and the top of the pickup poles. usually with the strings fretted at athe top, (high) fret.

Fender has Jaguar pickups at 0.078″ (2.00mm) on the treble side, and 0.094″ (2.4mm) on the bass side. Now I’m not sure if my pickup adjustment screws are too short. Perhaps the neck shim has pushed everything up and away from the scratchplate, or the Staytrem bridge, being taller, has lifted the strings well out of this adjustment range – but the best I can achieve is about 3.00mm on the treble side, and 3.75mm on the bass. Still – the pickups sound sweet. There’s not too much harshness to the top end, and there’s no wobble to the sound of a sustained note. (This can indicate a magnetic pole “dragging” on a string). I may look at getting some longer pickup adjustment screws – to see if it makes any improvement in raising the pickups towards Fender guidelines – but I’ll also need some higher foam springs to push the pickups higher out of the pickup routs. I’ll put it on the to-do list.

Nut slot cutting


The nut I purchased for this neck is a bone nut – crucially cut to fit the curved slot on the Allparts neck. I usually have a few spares to hand for any pattern of nut I work with. It’s far too easy to get this next bit wrong. Cut a string slot too deep and the string buzzes all the way up the neck. Leave it too high, and the action at the nut can make play difficult, and stuff up your tuning. Really though, it’s just a question of some accurate measurement, a bit of maths, slow and steady working, and a logical, tidy approach.

The nut I’m using comes pre-slotted, so I don’t have to worry about the string spacing. I just need to deepen and enlarge the existing slots to the correct dimensions. The ideal nut slot depth provides just enough string clearance at the first fret, when the second fret is held, and so on up the neck. Because of the neck relief, the critical clearance is therefore at that first fret. The first task is to work out the depth of the slots which will provide the correct clearance.


Fender recommends a clearance of 0.020″ (0.457mm) on the high “E” string, and 0.018″ (0.508mm) on the low ‘E’ string. Because the neck and nut follow a gentle curve. I usually assume the two middle strings to require a measurement, somewhere between the two – in this case 0.019″ (0.483mm). I also assume the “A’ string to be paired with the low “E”, and the “B” string to be paired with the high ‘ E”. These clearances will be in addition to the dimension required between the fingerboard and the top of the first fret – the ‘fret height’. This can be measured by holding a metal straight edge across the second and first frets to a point where it meets the nut. The actual clearance can be measured at that point, using feeler gauges – and the resulting measurements for each pair of strings is added to the required clearances, to provide a height for the location of the bottom of each string slot, above the fingerboard.

String slot dimension (bottom of slot above fingerboard) = Fret height + Clearance

This provides a series of target measurements across the strings, running from low “E” to high “E” – 0.058″, 0.058″, 0.057″, 0.057″, 0.056″, 0.056″.

These dimensions locate the bottom of each string slot above the fingerboard – cutting the slots down to this level will therefore deepen the slots. The finished slots should, ideally, be only approximately the depth of half a string diameter – so extra, unecessary material should, optimally, be removed. This ensures that the nut slots don’t bind. Binding can affect tuning, and can also snag strings – preventing them from returning to tune properly, whenever the tremolo is used. The best approach is to add a dimension equal to half a string diameter, to each of the slot depth dimensions above. That gives a second measurement – and the ideal total height of the nut at each slot. The measurements  can be marked out, and then joined together with a single pencil line. I can then pare away any unwanted nut material above this point. Given I use a heavy-bottom, custom light set of strings for my Fenders, the resultant required dimensions for the full height of the Jaguar nut work out to be, again from low “E” to high “E” – 0.084″, 0.079″, 0.073″, 0.069″, 0.064″, 0.062″.

I assemble combined thicknesses of feeler gauges to provide the correct measurement, and then mark the required height at each string with a pencil. The resulting line, shown in the photo above, will provide the line, down to which I can safely remove nut material, after I’ve cut the slots to the correct depth. It’s usually better to shape the nut after the slots have been shaped – so that’s the next job.


I cut the middle two slots first – then the treble and bass slots, in pairs, after that. So, selecting a series of feeler gauges to provide a 0.057″ clearance, I hold then onto the fingerboard to provide a physical, metal edge at the required slot depth. By working a special, slot-cutting file for the correct string gauges, from the fingerboard towards the headstock – it’s possible to feel when the file just touches the feeler gauges at the required depth. Once I feel the slightest scratch of the file against the steel of the gauge, I stop immediately – following on only to file a gently curving down slope on the headstock side of the nut. When the slot is cut, I find it helps to gently clean out the slot with a single thickness of fine grit paper. This helps to remove any sharp edges or loose residue.

Shaping the slots in the nut is a delicate business, and it takes time – so go easy. Ideally, the slot should gently slope away towards the headstock, so that the break point of the string is precisely at the face of the nut, just where the fingerboard begins. I always keep the gauges in place when filing – just to make sure I can’t accidentally cut the slots any deeper. Once one slot is completed, I move onto the next, and repeat until all six slots are cut to the correct depth, and are smooth and free from debris. It’s a good idea to test fit the strings at this point under proper tuning tension – just to make sure there are no unwanted buzzes, which might indicate something has gone wrong somewhere. If something sounds off, it’s usually either some dodgy maths, an accidental over-deepening of a slot, or a mistake in identifying high and low “E’s”. We’ve all done it, although we won’t all admit it.


I can now remove the excess nut material down to the line I marked earlier. You can probably see that the calculations result in a line marked a little above the, “half-a-string”, desired, mark – but that’s down to the accuracy of the pencil mark drawn on top of the feeler gauges. (and mine looks like it was done with a tar brush). It’s usually a millimeter or so above the actual point, since the pencil never seems to be sharp enough to get right in there. But that’s a good thing. So long as I take material down to the line and not over it – it’ll help provide a little safety tolerance.

Material is removed either by putting the nut in a vice, and then filing it away – or by holding the nut upside down and working away on a bit of 400 grit paper. Either way – go slow, and make sure you’re only removing excess material. Once enough has gone, I switch to a finer grit and smooth over – gradually working with finer and finer grades, until the nut is shaped and polished sufficiently.


After cleaning the nut slot, so it’s free of any dust or debris from cutting the slots – the nut can be finally fitted and held in place with two small dots of superglue. The nut may have to be replaced in time, and it should be possible to remove it with a sharp sideways tap. Super glue is ideal since it’s crystalline structure is fragile and it should break. You don’t want to use too much of any adhesive at the nut, however – since troublesome removal might damage the fingerboard edge or even the nut slot itself. A well shaped nut should sit in it’s slot without glue. If you have to use glue – use it very sparingly.

Fine tuning


With the nut in place, the strings can now be brought up to proper tension. Sliding the lock button across, to lock the tremolo plate in place, will help tuning – although further adjustment may, ultimately, have to be carried out at the tremolo plate to ensure that the lock position is optimal. Once the guitar is tuned, the button should be slid over to the “open” position where the tremolo is fully functional. If the guitar tuning should change, the adjustment screw on the tremolo plate needs to be turned until the guitar goes back into tune. That sets the optimal point for the slide switch. So long as the string tension remains the same, this will not need changing – although if a different set of strings is chosen or, perhaps, a different tuning is desired – then the process will need to be revisited, and the lock position re-aligned.

Intonation adjustment

The last step is to make the necessary adjustments so that the tuned strings – now set to their ideal paths – are adjusted to the correct lengths. Tuned and intonated strings will be in the proper relationship for correct tuning relationships, across the entire neck of the guitar. It’s a vital step, and when done correctly – it dramatically opens up the harmonics generated by the guitar. Personally – I find properly intonated guitars to be so much more powerful and “alive”. Properly setting up a guitar can be like buying a whole new instrument. When I played with the Citizens, and before I learned to do some of this myself, we always used to take our guitars down to Andy’s on Denmark Street in London. The difference with a proper, professional setup is amazing, and can take an ordinary, stock guitar to an entirely different level. Intonation is only part of the full set-up process, as you can see, but it’s one which is often overlooked entirely.


And it’s relatively simple. With all the other adjustments made, all I have to do is make each string the correct length between nut and bridge. The correct length will have the twelfth fret at a point exactly one half of the way between the nut and the bridge. Intonation adjustment is done at the bridge – by moving each individual string saddle forwards or backwards within the bridge mechanism. This effectively shortens or lengthens each string. The way to assess each string is to test the tuning by striking the string open, and again at the twelfth fret. The string needs to be accurate, and in tune, at both of these points, (since the 12th fret is a basic octave harmonic – located exactly halfway along the string).

Usually, if the open note is in tune, and the note at the 12th fret is sharp – then the overall string is too short. It’ll need lengthening by moving the saddle away from the headstock slightly. If flat – then vice versa. Adjustment can be made, and the test repeated – with further adjustment made in small increments until each string is precisely in tune when sounded both open, and at the 12th fret. With the Staytrem bridge, the adjustments are made to each individual saddle, via small hex screws on the side of the bridge. I like to use a chromatic tuner to get the micro-adjustments bang on.

With the guitar properly set up – the difference is noticeable. I can feel the difference in “slinkiness” and string tension that Jaguars are usually noted for. Now it’s a case of settling in all of the adjustments. “Playing-in” the guitar. Because all of the various set-up adjustments have small, potential, knock-on effects – it’s entirely possible that some of the basic steps may need to be repeated. Especially if any particular step has resulted in significant changes to the string geometry. However – any subsequently required changes should now be very small. I usually let everything settle down for a few weeks – before checking over the guitar again, and verifying each adjustment in the usual sequence. This period of “playing-in” is when you can really get to know an instrument and, having put the thing together myself – this is one of the most rewarding things. It really is a major perk of the whole do-it-yourself ethos. That combination of discovery, novelty, “I didn’t know it could do that!”, “Wow – listen to that!”, is what getting hold of a new instrument is all about. It’s like being let loose in the guitar shop all over again, but I can now test this particular instrument out knowing that I’ve put it together, and how I anticipated it to perform from the beginning. That’s particularly exciting. It’s all about learning. But it’s learning in a candy shop environment. Excuse me while I go try this one out.

I may be some time.

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