Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true). Pavel.