Big armatures problem....

http://members.ozemail.com.au/~wenke/half-body.blend

Here I used a skeleton that had some cylinders attached to it and some animations which I think I got from BlenderChar. It says it was made by Thachury. I got rid of everything except the skeleton and the empties. I’ve made half of a body and I found that if I parented the body to the skeleton (after assigning groups of vertices to bone names) the body would screw up… I found out how to mostly fix this… when I selected the skeleton and press tab to go in and out of edit mode, its positions would change - in edit mode its arms were out-stretched - but out of edit mode its arms were by its side. So I made its arms outstretched in and out of edit mode. Then I made the body’s arms line up with the skeleton and the arms no longer screwed up. Note that I’ve only put the vertices of the upper arms, chest, head and waist in groups at the moment.
The big problem now is the axis of the head is different in and out of edit mode. This means that when I parent the body to the armature the head screws up - it rotates to the side. I can’t rotate the head bone at all since it is always facing an empty… even if I go into pose mode. If I stop it tracking the empty then I can rotate it however I like… (but I want it to track the empty)
Basically the axes of the hand, feet and head bones have been rotated 90 degrees for some reason… if I select the armature and go into pose-mode and press F7 to see the animation buttons, I can fix the axes of individual hands, head or feet by pressing UpX/Y/Z… but when I do, some of the other axes of the hands/head/feet change!
I’ve tried using clear rotation in pose-mode - that doesn’t do anything. If I do it in normal mode, the skeleton turns into a twisted mess and I managed to untwist it but I still had the axis problem with the head/hands/feet… At the moment you can see the problem with the head by parenting the body to the skeleton and I think a similar problem would also happen with the feet - I just haven’t tried it…
Thanks if anyone can help.

The roll of the neck bone sounds like it’s off (blender occationaally guesses this wrong Though it usually happens on Feet)

In Edit mode hit “N” and the edit menu will come up and you can adjust the Roll.

DetectiveThorn

Bingo! Thanks dude.