I agree with @komodo
There is nothing wrong from a trigonometrical point of view with Tundraman's calculator, but there are a lot of areas where, in practice, things can be a little bit different and the cumulative effect is dramatic.
Almost all of my builds are through-necks and I always - as @komodo says - make sure I have the bridge and fretboard blank in my possesion and the planned fretwire dimensions first.
I'm sure there are better ways than I do it, but basically I draw the critical points full size. It only needs a few lines drawn with a decent length steel rule. The critical thing is knowing how much practical saddle adjustment is available to start with.
Probably more drawing than actually needed (but it helped me also envisage how deep the pickups needed to sit) but here is one of my drawings:
In the above photo:
Trust me - it's quicker to draw it than to explain it!
the hatched fretboard represents the total height of the fretboard and frets combined.
The pivot point - as Tundraman says, this is the point at which the neck joins the body - can be seen as the dot a few inches to the right of the fretboard end
The line broken by dots at the very top is the string, giving me the required action height target at the fretboard end and originating at fret height only at the nut
the short line on the left hand side with the writing next to it is where the top of the saddle needs to be at its lowest adjustment position (sitting below the string line a touch to give me a 1mm or so wiggle room)
The full line immediately below it is the 'zero angle' line, parallel with the tops of the frets
The ^ at the left hand side is at the scale length and, vertically, is where the bottom of the bridge (ie the top of the body) needs to be
Joining a line from the ^ to the pivot point, gives me the required neck angle