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The reason why I managed to keep the mesh groups in order before was that the changes I made only affected one or two mesh groups. And since Orbiter .msh format isn't binary but rather raw ASCII text, I could simply copy&paste the changes from separate msh file, essentially conducting surgery on it. This simply wasn't an option this time.Now I can only see Atlantis (despite the scenario has Columbia) and the textures are all over the place... That looks like a complete new thing which will require a massive intervention on the textures. Wouldn't it be better to keep the last mesh with maybe some minor tweaking. Most of it was ok and the hi res textures fitted quite well. Why this big change?
Every time you save a new msh file from AC3D or whatever your 3D editor might be, the mesh group order changes so the numbers that the animation codes uses are thrown off leading to the wrong things being animated. So to fix this, a new mesh resource header file (meshres for short) had to be generated. And this is baked into the overall SSU module ("SpaceShuttleUltra.dll") when you build the actual sources. So you can't just run the mesh resource generator ("ssumeshc") and replace the old one with the new and then run Orbiter. The sources have to be recompiled for the new meshres.h header to take effect.
So that's the reason why the sources have to be recompiled this time, just to many changes. Every time you invade the actual msh file like I have been doing, you risk breaking it completely requiring you to start over with the old msh file with no guarantee that you won't break it again.