Modeling in Blender To Import in Unity

If you are using Blender to make your models and Unity as your game engine it is important to note that the axis are different. 

Blender uses a right hand coordinate system, which means positive Z is up, positive Y is back, and positive X is right (but means left side of your model).

To back up this explanation go into Blender and make a new project. Before going to town and making an entire character (or whatever) press 1 on the numpad or change the view to front perspective. You'll notice that the Red Manipulator Arrow or X axis handle is now facing right. So this means that if you make a model make sure that it is facing you in this view.

Once you have your model all made and ready to go make sure the rotation and scale is applied. You can do this by holding Ctrl and pressing A and select rotation and scale. To check if this is not done press N to pull up the Properties Panel that displays all the info for location, rotation, and scale. Under the rotations it should read 0,0,0 and under scale 1,1,1 this means rotation and scale is applied.

If you make sure that this is thought out before starting on your game model project, then exporting it as an fbx and dragging it into Unity should be just perfect.

For Animations Use Blender or Unity?

With animations it depends on how complicating they are. Say if you are making a simple crate and want the lid to open you could just make the crate in Blender and do the animations in Unity using the Animation Curve Editor. For more complex animations use Blender and the Dope Sheet to create specific actions. Blender will have more range of tools to animate objects such as IK (inverse kinematics) and constraints

Click Here for a forum with a little more workflow explanation.

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