I'm currently trying some modding on systems, and i saw these coordinates used for position, however, i don't know where the reference lines are, and how this relates to distances on the map (say an obj1 has coordinates 1000,0,0 where could i find it then?)
Coordinates in .ini files use the x, y, z, setup. If you look at graph paper, and put a dot in the middle of it, you have four boxes. x = Right/Left. Right is positive, left is negative. So an X of 10000 = 10K to the right on your navmap in FL. Y is Up/Down. Up, as in, straight up in-game, not on your navmap. If you go straight up on your Y plane without changing X or Z, the object will be above you. Z controls Forward/Back. If Z = 10000, that means 10K in front of you.
So say you've got your graph paper flat on the table. Move your pencil right or left and you're altering the X plane, take the pencil off the paper and lift it and you're moving on the Y plane, and go away from you or back towards you on the paper and that is Z plane.
Most objects in FL all stay on the same plane. X and Z are altered, but Y is usually left alone. Y is used when you want objects to be above/below the normal plane.
It should also probably be mentioned that since there are different sized systems the same co-ordinates in one system will place an object on a different place on the map than in another system, as the map doesnt change it's grid system for systems of different sizes.
What Taz means is that -50000 = 50K to the left on the map. While on a small map that'll put the object on the very edge of the border or beyond the border, on a big map it'll only be about halfway between the center and the edge of the map. The coordinates specify distance units. 50000 = 50,000m = 50K So 1000, 0, 0 = 1K, 0K, 0K.
There is a file somewhere which defines the scale of the NavMap on a per-system basis, I can't remember which one(s) but it will be somewhere. Coordinates of objects are about 750x those that MS Paint would give. As an example, the NavMap will appear in MS Paint as 375x375 pixels. Equating and doubling this, to equal 282,000, gives you the entire width and height of the NavpMap at the normal scale, or in other words it is 141k from New York's sun to each system boundary.
In the case of Manhattan, you do it like this...
Take -33,150,-33,150 which is the approximate location of Manhattan as given by LI01.INI...
Take -33,150, divide it by 750 and add 187 to the final figure. This gives you 142. If you were to take a screen shot of New York and trim the image to 375x375, you should see that Manhattan is indeed at 142,142 pixels on the image.
Or, the other way around is take 142, deduct 187 and multiply by 750, to give -33,750. It's not precise but it should be good enough I think for general plotting.
You must account for the NavMapScale of the relevant system and multiply the coordinates by this before the above calculations (in this case New York is 1.0 so it doesn't matter).