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As requested you'll find a downloadable 3D skybox example in the description of this
video. This is for people who want to do island maps and are having trouble lining things
up. Looking at it may also help clear up the maths behind skyboxes. If you'd like to replace
the water texture with another, be sure to replace the one in the skybox with a texturescale
16 times smaller than the one in the level, so that it lines up.
There are some down-sides to this example map, though they can all be overcome with
some common sense and clever manipulation. Firstly, you CAN see where the world ends
and the skybox begins. This is partly because most water textures in Source don't reflect
skybox scenery, that they don't scale properly in the skybox and partly because HDR seems
to mess up the colours somewhat. Or at least, that's what I'm blaming it on. With my kyrenia
map I extended the level and included the near-by 'distant' scenery in the main level
to keep their reflections in-tact, and avoided walls like this one where the join is obvious.
You can always blend the line with props, or sticky out bits of wall. I'd advise against
making the lightmap scale in the skybox 16 times smaller, as although this will make
the shadows match up more accurately, it will significantly increase your map's filesize
and can cause glitches like this one here. Secondly, if you're going under water, THIS
will happen. You have a couple of choices- either you can prevent the player from going
under-water, or you can texture the far sides under-water with a texture, This will make
it foggy until you're up close to the edge, but can cause graphical glitches above the
surface, so you'll need to experiment with the colour. Another way is to texture the
edges of the water from within the skybox itself. You'll need to get the exact colour
of the murky water and create a custom texture for it, but doing so should make it seamless.
Any how, those are all your problems now, enjoy the vmf.