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Alright I've found some potential issues that you could fix for your model to work better!

When you're using the Paradox exporter you have to use the animation attribute on the root joint, which you do. However you need to separate the animations either by a new animation or by the attribute "none" to close an animation (you can add this by selecting the root joint and then go to Modify > Edit attribute.). You can also use different materials for different meshes, you need to set the PdxMeshShip shader on each of them.
When skinning the mesh you have to bind the skin to the root joint (highest in hierarchy) to each of the meshes, then paint the skin weights for each mesh to use the desired weights for each joint. For your model it's probably going to be 0 on every joint and 1 on the correct joint for that mesh.

Modeling pointers:
1. Textures are way too big for the level of detail on the model. Compare with the texture resolution of our battleships for example. If you will add much more detail to the texture then it might be reasonable to keep them at 2048x2048.
2. Use much more texture tiling.
3. Use plating details in normal map, this includes indents and edges.
 
I took another look and I got it to work in game, albeit with some shading/texture errors.

If that is what the wiki tutorial says then it's wrong and I'll take a look at it. You need to use "none" or another animation, then it will not be any space between animations. You don't have to restart the application after editing an attriute, although I don't know how the student version of Maya works in that regard.

Maya crashed because of a GPU animation evaluation bug in Maya 2016, you can fix it by going to Windows > Settings/Preferences > Preferences > Animation and at the top set Evaluation Mode to "Serial" and check "GPU Override".

Try out if that works for you!

PS: You have to set up the .asset- and .gfx-files to make it work in game, but since I already did that when trying I attached my files so you don't have to do it from scratch. :)
 

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Good that it works better, I'm afraid I don't know why it might render it the way it does, but look over the model and see if you can optimize it a little when it comes to vertex count and edge loop flow (they are a little everywhere and in strange angles right now).

You can't use several animations affecting the same bones, unfortunately, the only to do something like that is to have a separate mesh/entity with its own animations which you can attach your ship to and sync the animations, but that's very advanced, just try to get your model to look and animate correctly right now I'd say. :)