[phenixbb] How do different sections of TLS groups affect refinment

Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron