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As far as I know, the baxter API does not support having some joints in position mode, and other joints in velocity mode, so what you want to do is not possible.

However, for velocity mode, sending a cmd to set some joints to 0 radians/sec should work like anyone would expect. The behavior that "the arm falls down" says to me that your code may be triggering an emergency stop.

My advice is to go back to the original wobbler code, and make one small change at a time to determine where the problem is in your code.