
The reason for this was because when the biped was applied to the model, it used default settings to create envelopes - telling the program which vertices are "attached" to each part of the biped. Since the envelopes were not big enough, they missed some of the vertices further from the limb, and left them behind creating a stretching effect. However, if the envelopes are too big, they can also pull on vertices of other polygons you dont intend them to.
To fix this, I selected each part that was suffering from this problem, and then clicked on the modify panel, and clicked the "Physique" heading, then "Envelope". From here, I could modify the size of the envelopes to make sure they incorporated all of the vertices that should move with that limb.
Since I did not seperate the legs before applying the biped, the envelopes would sometimes interfere with the leg opposite, which did cause a bit of a problem. However, I managed to get around this by unlinking all of the vertices from the biped's legs, and then locking the vertices in the opposite leg as I manually applied the envelopes to them individually.

Once all of the envelopes were fixed, the Biped could be moved to manipulate my character properly.
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